Mercurial > repos > galaxyp > openms_digestormotif
changeset 10:bc7bd4710c4e draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
| author | galaxyp |
|---|---|
| date | Tue, 13 Oct 2020 19:52:20 +0000 |
| parents | 861833218c65 |
| children | 38676a2713f5 |
| files | 404-urls.patch DigestorMotif.xml OMSSAAdapter.patch PepNovoAdapter.patch filetypes.txt fill_ctd.py fill_ctd_clargs.py generate-foo.sh generate.sh hardcoded_params.json macros.xml macros_autotest.xml macros_discarded_auto.xml macros_test.xml prepare_test_data_manual.sh readme.md test-data.sh tool-data/pepnovo_models.loc.sample tool.conf tool_data_table_conf.xml.sample tool_data_table_conf.xml.test tools_blacklist.txt |
| diffstat | 22 files changed, 29819 insertions(+), 439 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/404-urls.patch Tue Oct 13 19:52:20 2020 +0000 @@ -0,0 +1,11 @@ +diff -ruN FeatureFinderSuperHirn.xml FeatureFinderSuperHirn.xml +--- FeatureFinderSuperHirn.xml 2020-10-02 12:06:56.398572301 +0200 ++++ FeatureFinderSuperHirn.xml 2020-10-02 12:07:31.511153834 +0200 +@@ -105,6 +105,6 @@ + <help><![CDATA[Finds mass spectrometric features in mass spectra. + + +-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureFinderSuperHirn.html]]></help> ++For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.6.0/html/UTILS_FeatureFinderSuperHirn.html]]></help> + <expand macro="references"/> + </tool>
--- a/DigestorMotif.xml Fri May 17 10:22:48 2019 -0400 +++ b/DigestorMotif.xml Tue Oct 13 19:52:20 2020 +0000 @@ -1,102 +1,113 @@ <?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> <!--Proposed Tool Section: [Utilities]--> -<tool id="DigestorMotif" name="DigestorMotif" version="2.3.0"> +<tool id="DigestorMotif" name="DigestorMotif" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>digests a protein database in-silico</description> <macros> <token name="@EXECUTABLE@">DigestorMotif</token> <import>macros.xml</import> + <import>macros_autotest.xml</import> + <import>macros_test.xml</import> </macros> - <expand macro="references"/> + <expand macro="requirements"/> <expand macro="stdio"/> - <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[DigestorMotif + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re + +## Preprocessing +mkdir in && +ln -s '$in' 'in/${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($in.ext)' +-out +'out/output.${gxy2omsext("idxml")}' -#if $param_in: - -in $param_in -#end if -#if $param_out: - -out $param_out -#end if -#if $param_missed_cleavages: - -missed_cleavages $param_missed_cleavages -#end if -#if $param_mass_accuracy: - -mass_accuracy $param_mass_accuracy -#end if -#if $param_min_length: - -min_length $param_min_length -#end if -#if $param_out_option: - -out_option $param_out_option -#end if -#if $param_enzyme: - -enzyme - #if " " in str($param_enzyme): - "$param_enzyme" - #else - $param_enzyme - #end if -#end if -#if $param_motif: - -motif "$param_motif" -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force -#end if -#end if -]]></command> +## Postprocessing +&& mv 'out/output.${gxy2omsext("idxml")}' '$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[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> + </configfiles> <inputs> - <param name="param_in" type="data" format="fasta" optional="False" label="FASTA input file" help="(-in) "/> - <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="1" label="the number of allowed missed cleavages" help="(-missed_cleavages) "/> - <param name="param_mass_accuracy" type="integer" value="1000" label="give your mass accuracy in pp" help="(-mass_accuracy) "/> - <param name="param_min_length" type="integer" value="6" label="minimum length of peptide" help="(-min_length) "/> - <param name="param_out_option" type="integer" value="1" label="indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + statistics)" help="(-out_option) "/> - <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) "> - <option value="Formic_acid">Formic_acid</option> + <param name="in" argument="-in" type="data" format="fasta" optional="false" label="FASTA input file" help=" select fasta data sets(s)"/> + <param name="missed_cleavages" argument="-missed_cleavages" type="integer" optional="true" min="0" value="1" label="the number of allowed missed cleavages" help=""/> + <param name="mass_accuracy" argument="-mass_accuracy" type="integer" optional="true" value="1000" label="give your mass accuracy in pp" help=""/> + <param name="min_length" argument="-min_length" type="integer" optional="true" value="6" label="minimum length of peptide" help=""/> + <param name="out_option" argument="-out_option" type="integer" optional="true" value="1" label="indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + statistics)" help=""/> + <param name="enzyme" argument="-enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help=""> <option value="Alpha-lytic protease">Alpha-lytic protease</option> - <option value="V8-E">V8-E</option> - <option value="unspecific cleavage">unspecific cleavage</option> - <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> - <option value="V8-DE">V8-DE</option> - <option value="leukocyte elastase">leukocyte elastase</option> - <option value="PepsinA">PepsinA</option> - <option value="Arg-C">Arg-C</option> - <option value="TrypChymo">TrypChymo</option> - <option value="no cleavage">no cleavage</option> - <option value="CNBr">CNBr</option> - <option value="Trypsin/P">Trypsin/P</option> + <option value="2-iodobenzoate">2-iodobenzoate</option> + <option value="iodosobenzoate">iodosobenzoate</option> + <option value="staphylococcal protease/D">staphylococcal protease/D</option> + <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> + <option value="Glu-C+P">Glu-C+P</option> + <option value="PepsinA + P">PepsinA + P</option> + <option value="cyanogen-bromide">cyanogen-bromide</option> + <option value="Clostripain/P">Clostripain/P</option> + <option value="Asp-N/B">Asp-N/B</option> + <option value="Asp-N_ambic">Asp-N_ambic</option> <option value="Chymotrypsin">Chymotrypsin</option> <option value="Chymotrypsin/P">Chymotrypsin/P</option> - <option value="Asp-N_ambic">Asp-N_ambic</option> + <option value="CNBr">CNBr</option> + <option value="Formic_acid">Formic_acid</option> <option value="Lys-C">Lys-C</option> - <option value="Trypsin" selected="true">Trypsin</option> - <option value="Asp-N">Asp-N</option> + <option value="Lys-N">Lys-N</option> + <option value="Lys-C/P">Lys-C/P</option> + <option value="PepsinA">PepsinA</option> + <option value="TrypChymo">TrypChymo</option> + <option value="Trypsin/P">Trypsin/P</option> + <option value="V8-DE">V8-DE</option> + <option value="proline endopeptidase">proline endopeptidase</option> + <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> + <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> + <option value="no cleavage">no cleavage</option> + <option value="unspecific cleavage">unspecific cleavage</option> + <option value="Arg-C">Arg-C</option> <option value="Arg-C/P">Arg-C/P</option> - <option value="proline endopeptidase">proline endopeptidase</option> - <option value="Asp-N/B">Asp-N/B</option> - <option value="Lys-N">Lys-N</option> - <option value="2-iodobenzoate">2-iodobenzoate</option> - <option value="Lys-C/P">Lys-C/P</option> + <option value="Asp-N">Asp-N</option> + <option value="V8-E">V8-E</option> + <option value="leukocyte elastase">leukocyte elastase</option> + <option value="Trypsin" selected="true">Trypsin</option> + <expand macro="list_string_san"/> </param> - <param name="param_motif" type="text" size="30" value="M" label="the motif for the restricted peptidome" help="(-motif) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <param name="motif" argument="-motif" type="text" optional="true" value="M" label="the motif for the restricted peptidome" help=""> + <expand macro="list_string_san"/> </param> - <expand macro="advanced_options"> - <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + <expand macro="adv_opts_macro"> + <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> + <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san"/> + </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="param_out" format="idxml"/> + <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>digests a protein database in-silico + <tests> + <expand macro="autotest_DigestorMotif"/> + <expand macro="manutest_DigestorMotif"/> + </tests> + <help><![CDATA[digests a protein database in-silico -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_DigestorMotif.html</help> +For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_DigestorMotif.html]]></help> + <expand macro="references"/> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OMSSAAdapter.patch Tue Oct 13 19:52:20 2020 +0000 @@ -0,0 +1,10 @@ +--- OMSSAAdapter.xml 2020-06-16 15:51:40.315400730 +0200 ++++ /tmp/OMSSAAdapter.xml 2020-06-16 15:50:23.536086074 +0200 +@@ -22,6 +22,7 @@ + mkdir database && + ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && + ++makeblastdb -dbtype prot -in 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && + ## Main program call + + set -o pipefail &&
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PepNovoAdapter.patch Tue Oct 13 19:52:20 2020 +0000 @@ -0,0 +1,35 @@ +--- PepNovoAdapter.xml 2020-05-12 15:55:24.712831518 +0200 ++++ /tmp/PepNovoAdapter.xml 2020-05-12 15:36:31.267276757 +0200 +@@ -42,8 +42,13 @@ + </configfiles> + <inputs> + <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> +- <param name="model_directory" argument="-model_directory" type="text" optional="false" value="" label="Name of the directory where the model files are kept" help=""> +- <expand macro="list_string_san"/> ++ <param name="model_directory" argument="-model_directory" type="select" optional="false" label="Name of the directory where the model files are kept" help=""> ++ <options from_data_table="pepnovo_models"> ++ <column name="name" index="0"/> ++ <column name="value" index="2"/> ++ <filter type="unique_value" name="unique_set" column="0"/> ++ <validator type="no_options" message="No model directory available"/> ++ </options> + </param> + <param name="correct_pm" argument="-correct_pm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find optimal precursor mass and charge values" help=""/> + <param name="use_spectrum_charge" argument="-use_spectrum_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not correct charge" help=""/> +@@ -51,8 +56,14 @@ + <param name="no_quality_filter" argument="-no_quality_filter" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not remove low quality spectra" help=""/> + <param name="fragment_tolerance" argument="-fragment_tolerance" type="float" optional="true" value="-1.0" label="The fragment tolerance (between 0 and 0.75 Da" help="Set to -1.0 to use model's default setting)"/> + <param name="pm_tolerance" argument="-pm_tolerance" type="float" optional="true" value="-1.0" label="The precursor mass tolerance (between 0 and 5.0 Da" help="Set to -1.0 to use model's default setting)"/> +- <param name="model" argument="-model" type="text" optional="true" value="CID_IT_TRYP" label="Name of the model that should be used" help=""> +- <expand macro="list_string_san"/> ++ <param name="model" argument="-model" type="select" label="Name of the model that should be used" help=""> ++ <options from_data_table="pepnovo_models"> ++ <column name="name" index="1"/> ++ <column name="value" index="1"/> ++ <filter type="param_value" ref="model_directory" column="2"/> ++ <filter type="unique_value" column="1"/> ++ <validator type="no_options" message="No model available"/> ++ </options> + </param> + <param name="digest" argument="-digest" display="radio" type="select" optional="false" label="Enzyme used for digestion (default TRYPSIN)" help=""> + <option value="TRYPSIN" selected="true">TRYPSIN</option>
--- a/filetypes.txt Fri May 17 10:22:48 2019 -0400 +++ b/filetypes.txt Tue Oct 13 19:52:20 2020 +0000 @@ -1,29 +1,85 @@ -# CTD type # Galaxy type # Long Galaxy data type # Mimetype -csv tabular galaxy.datatypes.tabular:Tabular -fasta fasta galaxy.datatypes.sequence:Fasta -FASTA fasta galaxy.datatypes.sequence:Fasta -ini txt galaxy.datatypes.data:Text -txt txt galaxy.datatypes.data:Text -options txt galaxy.datatypes.data:Text -grid grid galaxy.datatypes.data:Grid -html html galaxy.datatypes.text:Html text/html -HTML html galaxy.datatypes.text:Html text/html -TraML traml galaxy.datatypes.proteomics:TraML application/xml -traML traml galaxy.datatypes.proteomics:TraML application/xml -XML xml galaxy.datatypes.xml:GenericXml application/xml -consensusXML consensusxml galaxy.datatypes.proteomics:ConsensusXML application/xml -edta tabular galaxy.datatypes.tabular:Tabular -featureXML featurexml galaxy.datatypes.proteomics:FeatureXML application/xml -idXML idxml galaxy.datatypes.proteomics:IdXML application/xml -mzML mzml galaxy.datatypes.proteomics:MzML application/xml -mzXML mzxml galaxy.datatypes.proteomics:MzXML application/xml -pepXML pepxml galaxy.datatypes.proteomics:PepXml application/xml -qcML qcml galaxy.datatypes.xml:GenericXml application/xml -trafoXML trafoxml galaxy.datatypes.xml:GenericXml application/xml -tsv tabular galaxy.datatypes.tabular:Tabular -xsd txt galaxy.datatypes.data:Text -mzq mzq galaxy.datatypes.proteomics:MzQuantML application/xml -msp msp galaxy.datatypes.proteomics:Msp -mzid mzid galaxy.datatypes.proteomics:MzIdentML application/xml -png png galaxy.datatypes.images:Png image/png -mgf mgf galaxy.datatypes.proteomics:Mgf +# CTD type # Galaxy type +# the following lines need to be at the top in order to ensure +# correct translation Galaxy->CTD type for the ambiguous cases +# (should only be relevant for the autogenerated tests [which +# do not set the ftype of the inputs]) +txt txt +tsv tabular + +##analysisXML +# XTandemAdapter output is named xml in OMS (which is to unspecific) and bioml in Galaxy .. so this is renamed via hardcoded parameters +bioml xml +consensusXML consensusxml +# TODO csv is problematic, since csv often actually means tsv .. but not always +csv csv +##dat +dta dta +dta2d dta2d +edta edta +fa fasta +fas fasta +fasta fasta +FASTA fasta +featureXML featurexml +featurexml featurexml +# fid +html html +HTML html +idXML idxml +##ini txt +json json +kroenik kroenik +mascotXML mascotxml +mgf mgf +mrm mrm +ms sirius.ms +ms2 ms2 +msp msp +mzData mzdata +mzid mzid +# important to have mzML first, since LuciphorAdapter is case sensitive https://github.com/OpenMS/OpenMS/issues/4444 +mzML mzml +mzml mzml +mzq mzq +mzTab mztab +mzXML mzxml +novor txt +obo obo +# I guess this is the idXML output of omssa +omssaXML idxml +osw osw +OSW osw +params txt +paramXML paramxml +fasta peff +peplist peplist +# TODO pep.xml should be removed with OMS 2.6 https://github.com/OpenMS/OpenMS/pull/4541 .. but still in the tests +pep.xml pepxml +pepXML pepxml +png png +PNG png +protXML protxml +psms psms +# TODO implement or use +# psq +pqp pqp +qcML qcml +spec.xml spec.xml +splib splib +sqMass sqmass +tandem.xml tandem +trafoXML trafoxml +traML traml +TraML traml +tab tabular +## MOVED TO TOP txt txt +raw thermo.raw +## xls: SpectraSTSearchAdapter https://github.com/OpenMS/OpenMS/pull/4419 +xls tsv +XML xml +xml xml +xquest.xml xquest.xml +xsd xml + +# TODO needs to be implemented, needs to be below xml in order that Galaxy->OMS mapping gives xml +# cachedMzML xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fill_ctd.py Tue Oct 13 19:52:20 2020 +0000 @@ -0,0 +1,196 @@ +import collections +import json +import operator +import os +import re +import subprocess +import sys +from functools import reduce # forward compatibility for Python 3 + +from CTDopts.CTDopts import ( + _Choices, + _InFile, + _Null, + _NumericRange, + CTDModel +) + + +def getFromDict(dataDict, mapList): + return reduce(operator.getitem, mapList, dataDict) + + +def setInDict(dataDict, mapList, value): + getFromDict(dataDict, mapList[:-1])[mapList[-1]] = value + + +def mergeDicts(d, e): + """ + insert values from the dict e into dict d + no values of d are overwritten + """ + for k, v in e.items(): + if (k in d and isinstance(d[k], dict) and isinstance(e[k], collections.abc.Mapping)): + mergeDicts(d[k], e[k]) + elif k not in d and not isinstance(e[k], collections.abc.Mapping): + d[k] = e[k] + else: + sys.stderr.write("fill_ctd.py: could not merge key %s for %s in %s" % (k, d, e)) + sys.exit(1) + + +def _json_object_hook_noenvlookup(d): + return _json_object_hook(d, envlookup=False) + + +def _json_object_hook(d, envlookup=True): + """ + wee helper to transform the json written by galaxy + while loading + - True/False (bool objects) -> "true"/"false" (lowercase string) + - data inputs with multiple and optional true give [None] if no file is given -> [] + - None -> "" (empty string) + - replace bash expressions (if envlookup is True): + - environment variables (need to consist capital letters and _) by their value + - expressions + """ + for k in d.keys(): + # if type(d[k]) is bool: + # d[k] = str(d[k]).lower() + # else + if type(d[k]) is list and len(d[k]) == 1 and d[k][0] is None: + d[k] = [] + elif d[k] is None: + d[k] = "" + elif envlookup and type(d[k]) is str and d[k].startswith("$"): + m = re.fullmatch(r"\$([A-Z_]+)", d[k]) + if m: + d[k] = os.environ.get(m.group(1), "") + continue + m = re.fullmatch(r"\$(\{[A-Z_]+):-(.*)\}", d[k]) + if m: + d[k] = os.environ.get(m.group(1), m.group(2)) + continue + + try: + p = subprocess.run("echo %s" % d[k], shell=True, check=True, stdout=subprocess.PIPE, encoding="utf8") + d[k] = p.stdout.strip() + except subprocess.CalledProcessError: + sys.stderr.write("fill_ctd error: Could not evaluate %s" % d[k]) + continue + return d + + +def qstring2list(qs): + """ + transform a space separated string that is quoted by " into a list + """ + lst = list() + qs = qs.split(" ") + quoted = False + for p in qs: + if p == "": + continue + if p.startswith('"') and p.endswith('"'): + lst.append(p[1:-1]) + elif p.startswith('"'): + quoted = True + lst.append(p[1:] + " ") + elif p.endswith('"'): + quoted = False + lst[-1] += p[:-1] + else: + if quoted: + lst[-1] += p + " " + else: + lst.append(p) + return lst + + +def fix_underscores(args): + if type(args) is dict: + for k in list(args.keys()): + v = args[k] + if type(v) is dict: + fix_underscores(args[k]) + if k.startswith("_"): + args[k[1:]] = v + del args[k] + elif type(args) is list: + for i, v in enumerate(args): + if type(v) is dict: + fix_underscores(args[i]) + + +input_ctd = sys.argv[1] + +# load user specified parameters from json +with open(sys.argv[2]) as fh: + args = json.load(fh, object_hook=_json_object_hook_noenvlookup) + +# load hardcoded parameters from json +with open(sys.argv[3]) as fh: + hc_args = json.load(fh, object_hook=_json_object_hook) + +# insert the hc_args into the args +mergeDicts(args, hc_args) + +if "adv_opts_cond" in args: + args.update(args["adv_opts_cond"]) + del args["adv_opts_cond"] + +# IDMapper has in and spectra:in params, in is used in out as format_source", +# which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493" +# therefore hardcoded params change the name of spectra:in to spectra:_in +# which is corrected here again +# TODO remove once PR is in and adapt profile accordingly +fix_underscores(args) + +model = CTDModel(from_file=input_ctd) + +# transform values from json that correspond to +# - old style booleans (string + restrictions) -> transformed to a str +# - new style booleans that get a string (happens for hidden parameters [-test]) +# are transformed to a bool +# - unrestricted ITEMLIST which are represented as strings +# ("=quoted and space separated) in Galaxy -> transform to lists +# - optional data input parameters that have defaults and for which no +# value is given -> overwritte with the default +for p in model.get_parameters(): + + # check if the parameter is in the arguments from the galaxy tool + # (from the json file(s)), since advanced parameters are absent + # if the conditional is set to basic parameters + try: + getFromDict(args, p.get_lineage(name_only=True)) + except KeyError: + # few tools use dashes in parameters which are automatically replaced + # by underscores by Galaxy. in these cases the dictionary needs to be + # updated (better: then dash and the underscore variant are in the dict) + # TODO might be removed later https://github.com/OpenMS/OpenMS/pull/4529 + try: + lineage = [_.replace("-", "_") for _ in p.get_lineage(name_only=True)] + val = getFromDict(args, lineage) + except KeyError: + continue + else: + setInDict(args, p.get_lineage(name_only=True), val) + + if p.type is str and type(p.restrictions) is _Choices and set(p.restrictions.choices) == set(["true", "false"]): + v = getFromDict(args, p.get_lineage(name_only=True)) + setInDict(args, p.get_lineage(name_only=True), str(v).lower()) + elif p.type is bool: + v = getFromDict(args, p.get_lineage(name_only=True)) + if isinstance(v, str): + v = (v.lower() == "true") + setInDict(args, p.get_lineage(name_only=True), v) + elif p.is_list and (p.restrictions is None or type(p.restrictions) is _NumericRange): + v = getFromDict(args, p.get_lineage(name_only=True)) + if type(v) is str: + setInDict(args, p.get_lineage(name_only=True), qstring2list(v)) + elif p.type is _InFile and not (p.default is None or type(p.default) is _Null): + v = getFromDict(args, p.get_lineage(name_only=True)) + if v in [[], ""]: + setInDict(args, p.get_lineage(name_only=True), p.default) + +model.write_ctd(input_ctd, arg_dict=args)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fill_ctd_clargs.py Tue Oct 13 19:52:20 2020 +0000 @@ -0,0 +1,40 @@ +#!/usr/bin/env python3 +from argparse import ArgumentParser +from io import StringIO + +from CTDopts.CTDopts import ( + CTDModel, + ModelTypeError, + Parameters +) + +if __name__ == "__main__": + # note add_help=False since otherwise arguments starting with -h will + # trigger an error (despite allow_abbreviate) + parser = ArgumentParser(prog="fill_ctd_clargs", + description="fill command line arguments" + "into a CTD file and write the CTD file to", + add_help=False, allow_abbrev=False) + parser.add_argument("--ctd", dest="ctd", help="input ctd file", + metavar='CTD', default=None, required=True) + args, cliargs = parser.parse_known_args() + # load CTDModel + model = None + try: + model = CTDModel(from_file=args.ctd) + except ModelTypeError: + pass + try: + model = Parameters(from_file=args.ctd) + except ModelTypeError: + pass + assert model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ctd) + + # get a dictionary of the ctd arguments where the values of the parameters + # given on the command line are overwritten + margs = model.parse_cl_args(cl_args=cliargs, ignore_required=True) + + # write the ctd with the values taken from the dictionary + out = StringIO() + ctd_tree = model.write_ctd(out, margs) + print(out.getvalue())
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate-foo.sh Tue Oct 13 19:52:20 2020 +0000 @@ -0,0 +1,222 @@ +#!/usr/bin/env bash + +# parse test definitions from OpenMS sources for a tool with a given id +function get_tests2 { + id=$1 + >&2 echo "generate tests for $id" + echo '<xml name="autotest_'"$id"'">' + + # get the tests from the CMakeLists.txt + # 1st remove some tests + # - OpenSwathMzMLFileCacher with -convert_back argumen https://github.com/OpenMS/OpenMS/issues/4399 + # - IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differentlt + # - several tools with duplicated input (leads to conflict when linking) + # - TOFCalibration inputs we extension (also in prepare_test_data) https://github.com/OpenMS/OpenMS/pull/4525 + # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456) + # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed) + # - some input files are originally in a subdir (degenerated cases/), but not in test-data + # - SeedListGenerator: https://github.com/OpenMS/OpenMS/issues/4404 + # - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet) + # - FeatureFinderIdentification name clash of two tests https://github.com/OpenMS/OpenMS/pull/5002 + # - TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010 + CMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | + sed 's@${DATA_DIR_SHARE}/@@g' | + grep -v 'OpenSwathMzMLFileCacher .*-convert_back' | + sed 's/${TMP_RIP_PATH}/""/' | + grep -v "MaRaClusterAdapter.*-consensus_out"| + grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " | + sed 's@degenerate_cases/@@g' | + grep -v 'TOPP_SeedListGenerator_3"' | + egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"' | + egrep -v '"TOPP_FeatureFinderIdentification_4"' | + sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/') + + +# grep -v 'FileFilter.*-spectra:select_polarity ""' | +# grep -v 'MassTraceExtractor_2.ini ' | +# grep -v "FileMerger_6_input2.mzML.*FileMerger_6_input2.mzML" | +# grep -v "IDMerger_1_input1.idXML.*IDMerger_1_input1.idXML" | +# grep -v "degenerated_empty.idXML.*degenerated_empty.idXML" | +# grep -v "FeatureLinkerUnlabeledKD_1_output.consensusXML.*FeatureLinkerUnlabeledKD_1_output.consensusXML" | +# grep -v "FeatureLinkerUnlabeledQT_1_output.consensusXML.*FeatureLinkerUnlabeledQT_1_output.consensusXML" | + + # 1st part is a dirty hack to join lines containing a single function call, e.g. + # addtest(.... + # ....) + echo "$CMAKE" | sed 's/#.*//; s/^\s*//; s/\s*$//' | grep -v "^#" | grep -v "^$" | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | + grep -iE "add_test\(\"(TOPP|UTILS)_.*/$id " | egrep -v "_prepare\"|_convert|WRITEINI|WRITECTD|INVALIDVALUE" | while read -r line + do + line=$(echo "$line" | sed 's/add_test("\([^"]\+\)"/\1/; s/)$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g') + # >&2 echo $line + test_id=$(echo "$line" | cut -d" " -f 1) + tool_id=$(echo "$line" | cut -d" " -f 2) + if [[ $test_id =~ _out_?[0-9]? ]]; then + >&2 echo " skip $test_id $line" + continue + fi + if [[ ${id,,} != ${tool_id,,} ]]; then + >&2 echo " skip $test_id ($id != $tool_id) $line" + continue + fi + + #remove tests with set_tests_properties(....PROPERTIES WILL_FAIL 1) + if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then + >&2 echo " skip failing "$test_id + continue + fi + tes=" <test>\n" + line=$(fix_tmp_files "$line") + line=$(unique_files "$line") + # >&2 echo $line + #if there is an ini file then we use this to generate the test + #otherwise the ctd file is used + #other command line parameters are inserted later into this xml + if grep -lq "\-ini" <<<"$line"; then + ini=$(echo $line | sed 's/.*-ini \([^ ]\+\).*/\1/') + ini="test-data/$ini" + else + ini="ctd/$tool_id.ctd" + fi + cli=$(echo $line |cut -d" " -f3- | sed 's/-ini [^ ]\+//') + + ctdtmp=$(mktemp) + #echo python3 fill_ctd_clargs.py --ctd $ini $cli + # using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"]) + # >&2 echo "python3 fill_ctd_clargs.py --ctd $ini $cli" + eval "python3 fill_ctd_clargs.py --ctd $ini $cli" > "$ctdtmp" + # echo $ctdtmp + # >&2 cat $ctdtmp + testtmp=$(mktemp) + python3 $CTDCONVERTER/convert.py galaxy -i $ctdtmp -o $testtmp -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib > /dev/null + cat $testtmp | grep -v '<output.*file=""' # | grep -v 'CHEMISTRY/' + rm $ctdtmp $testtmp + + #> /dev/null + + #rm $testtmp + done + echo '</xml>' +} + +#some tests use the same file twice which does not work in planemo tests +#hence we create symlinks for each file used twice +function unique_files { + line=$@ + for arg in $@ + do + if [[ ! -f "test-data/$arg" ]]; then + continue + fi + cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n')) + while [[ $cnt -gt 1 ]]; do + new_arg=$(echo $arg | sed "s/\(.*\)\./\1_$cnt./") + ln -fs $arg test-data/$new_arg + line=$(echo $line | sed "s/\($arg.*\)$arg/\1$new_arg/") + cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n')) + done + done + + echo $line +} + +# options of out_type selects need to be fixed to Galaxy data types +function fix_out_type { + grep "^$1" "$2" | awk '{print $2}' +} + +#OpenMS tests output to tmp files and compare with FuzzyDiff to the expected file. +#problem: the extension of the tmp files is unusable for test generation. +#unfortunately the extensions used in the DIFF lines are not always usable for the CLI +#(e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt) +#this function replaces the tmp file by the expected file. +function fix_tmp_files { +# >&2 echo "FIX $line" + ret="" + for a in $@; do + if [[ ! $a =~ .tmp$ ]]; then + ret="$ret $a" + continue + fi +# >&2 echo " a "$a + g=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep '\${DIFF}.*'"$a") +# >&2 echo " g "$g + in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$g) + # >&2 echo " in1 "$in1 + if [[ "$a" != "$in1" ]]; then + ret="$ret $a" + continue + fi + in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$g) + in2=$(basename $in2 | sed 's/)$//') + # >&2 echo " in2 "$in2 + if [[ -f "test-data/$in2" ]]; then + ln -fs "$in1" "test-data/$in2" + ret="$ret $in2" + else + ret="$ret $a" + fi + done +# >&2 echo "--> $ret" + echo "$ret" +} + +function link_tmp_files { + # note this also considers commented lines (starting with a #) + # because of tests where the diff command is commented and we + # still want to use the extension of these files + cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's/^\s*//; s/\s*$//' | grep -v "^$" | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep "\${DIFF}" | while read -r line + do + in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$line) + in1=$(basename $in1 | sed 's/)$//') + in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$line) + in2=$(basename $in2 | sed 's/)$//') + if [[ "$in1" == "$in2" ]]; then + >&2 echo "not linking equal $in1 $in2" + continue + fi + ln -f -s $in1 test-data/$in2 + done + for i in test-data/*.tmp + do + if [ ! -e test-data/$(basename $i .tmp) ]; then + ln -s $(basename $i) test-data/$(basename $i .tmp) + #ln -s $(basename $i) test-data/$(basename $i .tmp) + else + ln -fs $(basename $i) test-data/$(basename $i .tmp) + fi + done +} + + + +# parse data preparation calls from OpenMS sources for a tool with a given id +function prepare_test_data { +# id=$1 +# | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?" + +# TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010 + cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's/#.*$//'| sed 's/^\s*//; s/\s*$//' | grep -v "^$" | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | + sed 's/degenerate_cases\///' | + egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | + grep add_test | + egrep "TOPP|UTILS" | + sed 's@${DATA_DIR_SHARE}/@@g;'| + sed 's@${TMP_RIP_PATH}@dummy2.tmp@g'| + sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'| + sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' | + while read line + do + test_id=$(echo "$line" | sed 's/add_test(//; s/"//g; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f1) + + if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then + >&2 echo " skip failing "$test_id + continue + fi + + line=$(echo "$line" | sed 's/add_test("//; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f2-) + # line="$(fix_tmp_files $line)" + echo 'echo executing "'$test_id'"' + echo "$line > $test_id.stdout 2> $test_id.stderr" + echo "if [[ \"\$?\" -ne \"0\" ]]; then >&2 echo '$test_id failed'; >&2 echo -e \"stderr:\n\$(cat $test_id.stderr | sed 's/^/ /')\"; echo -e \"stdout:\n\$(cat $test_id.stdout)\";fi" + done +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate.sh Tue Oct 13 19:52:20 2020 +0000 @@ -0,0 +1,76 @@ +#!/usr/bin/env bash + +VERSION=2.6 +FILETYPES="filetypes.txt" +PROFILE="20.05" +## FILETYPES_RE=$(grep -v "^#" $FILETYPES | grep -v "^$" | cut -f 1 -d" " | tr '\n' '|' | sed 's/|$//'| sed 's/|/\\|/g') + +export tmp=$(mktemp -d) +export CTDCONVERTER="$tmp/CTDConverter" + +############################################################################### +## reset old data +############################################################################### +# rm $(ls *xml |grep -v macros) +# rm -rf ctd +# mkdir -p ctd +# echo "" > prepare_test_data.sh + +############################################################################### +## generate tests +## also creates +## - conda environment (for executing the binaries) and +## - the git clone of OpenMS (for generating the tests) +## - ctd files +############################################################################### +bash ./test-data.sh ./macros_autotest.xml + +############################################################################### +## get the +## - conda package (for easy access and listing of the OpenMS binaries), +############################################################################### +# if [ ! -d $OPENMSPKG ]; then +# mkdir $OPENMSPKG/ +# wget -P $OPENMSPKG/ "$CONDAPKG" +# tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C OpenMS$VERSION-pkg/ +# rm $OPENMSPKG/"$(basename $CONDAPKG)" +# fi + +############################################################################### +## Get python libaries for CTD -> Galaxy conversion +## TODO fix to main repo OR conda packkage if PRs are merged +############################################################################### +# if [ ! -d CTDopts ]; then +# # git clone https://github.com/genericworkflownodes/CTDopts CTDopts +# git clone -b topic/no-1-2x https://github.com/bernt-matthias/CTDopts CTDopts +# fi +if [ ! -d $CTDCONVERTER ]; then + #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter + git clone -b topic/cdata https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER +fi +# export PYTHONPATH=$(pwd)/CTDopts +############################################################################### +## conversion ctd->xml +############################################################################### + +find . -maxdepth 0 -name "[A-Z]*xml" -delete +source $(dirname $(which conda))/../etc/profile.d/conda.sh +conda activate $tmp/OpenMS$VERSION-env +python $CTDCONVERTER/convert.py galaxy -i ctd/*ctd -o ./ -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p hardcoded_params.json --test-macros macros_autotest.xml --test-macros-prefix autotest_ --test-macros macros_test.xml --test-macros-prefix manutest_ --tool-version $VERSION --tool-profile $PROFILE > convert.out 2> convert.err +if [[ "$?" -ne "0" ]]; then >&2 echo 'CTD -> XML conversion failed'; >&2 echo -e "stderr:\n$(cat convert.err)"; fi +conda deactivate + +patch PepNovoAdapter.xml < PepNovoAdapter.patch +patch OMSSAAdapter.xml < OMSSAAdapter.patch + +# https://github.com/OpenMS/OpenMS/pull/4984 +sed -i -e 's@http://www.openms.de/documentation/@http://www.openms.de/doxygen/release/2.6.0/html/@' ./*xml +# https://github.com/OpenMS/OpenMS/pull/4984#issuecomment-702641976 +patch -p0 <404-urls.patch + +# #-b version log debug test in_type executable pepnovo_executable param_model_directory rt_concat_trafo_out param_id_pool + +# for i in A-E F-H I-L M-N O-P Q-Z +# do +# planemo t [$i]*xml --galaxy_branch release_20.05 --galaxy_python_version 3.7 --test_output $i.html --test_output_json $i.json & +# done
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hardcoded_params.json Tue Oct 13 19:52:20 2020 +0000 @@ -0,0 +1,236 @@ +{ + "#": "blacklist parameters", + + "version": [{"value": "@"}], + "debug": [{"value": "@"}], + "algorithm:debug": [{"value": "@"}], + "java_memory": [{"value": "@"}], + "java_permgen": [{"value": "@"}], + "#": "type of input is always determined from the file extension ", + "in_type": [{"value": "@"}], + + "#": "tool specific blacklist parameters", + + "convert_back": [{"value": "@", "tools": ["OpenSwathMzMLFileCacher"]}], + "NET_executable": [{ + "value": "@", + "tools": ["FileConverter"] + }], + + + "params_file": [{"value": "@", "tools": ["SpectraSTSearchAdapter"]}], + + "#": "TODO not usable in 2.5 https://github.com/OpenMS/OpenMS/issues/4456, corresponding test currently disabled", + "consensus_out": [{"value": "@", "tools": ["MaRaClusterAdapter"]}], + "#": "TODO would need treatment as prefix-output", + "output_directory": [{"value": "@", "tools": ["MaRaClusterAdapter"]}], + + "#": "hardcode parameter values", + + "comet_version": [{ + "value":"2016.01 rev. 3" + }], + "comet_executable": [{ + "value":"comet" + }], + "crux_executable": [{ + "value": "crux" + }], + "fido_executable": [{ + "value":"Fido" + }], + "fidocp_executable": [{ + "value":"FidoChooseParameters" + }], + "maracluster_executable": [{ + "value":"/home/berntm/projects/tools-galaxyp/tools/openms/OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster" + }], + "mascot_directory": [{ + "value":"TODO" + }], + "myrimatch_executable": [{ + "value":"myrimatch" + }], + "omssa_executable": [{ + "value":"$(dirname $(realpath $(which omssacl)))/omssacl" + }], + "ThermoRaw_executable": [{ + "value": "ThermoRawFileParser.exe", + "tools": ["FileConverter"] + }], + "pepnovo_executable": [{ + "value":"pepnovo" + }], + "percolator_executable": [{ + "value":"percolator" + }], + "xtandem_executable": [{ + "value":"xtandem" + }], + "executable": [ + { + "value":"$(dirname $(realpath $(which luciphor2)))/luciphor2.jar", + "tools": ["LuciphorAdapter"] + }, { + "value":"/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar", + "tools": ["MSFraggerAdapter"] + }, { + "value":"$(msgf_plus -get_jar_path)", + "tools": ["MSGFPlusAdapter"] + }, { + "value": "/home/berntm/Downloads/novor/lib/novor.jar", + "tools": ["NovorAdapter"] + }, { + "value":"$(which sirius)", + "tools": ["SiriusAdapter", "AssayGeneratorMetabo"] + }, { + "value":"spectrast", + "tools": ["SpectraSTSearchAdapter"] + } + ], + "r_executable": [{ + "value":"R" + }], + "rscript_executable": [{ + "value":"Rscript" + }], + "java_executable": [{ + "value":"java" + }], + "log": [{ + "value":"log.txt" + }], + "tempDirectory": [{ + "value":"$TMP_DIR" + }], + "temp_data_directory": [{ + "value":"$TMP_DIR" + }], + "algorithm:Preprocessing:tmp_dir": [{ + "value":"$TMP_DIR" + }], + "no_progress": [{ + "value": true + }], + "#": "only used in LuciphorAdapter at the moment, inconsistency will be fixed", + "num_threads": [{ + "value":"${GALAXY_SLOTS:-1}" + }], + "threads": [{ + "value": "${GALAXY_SLOTS:-1}" + }], + "sirius:cores": [{ + "value": "${GALAXY_SLOTS:-1}" + }], + + "#": "hardcode the outer loop threads for OpenSwathWorkflow", + "outer_loop_threads": [{ + "value": "1", + "tools": ["OpenSwathWorkflow"] + }], + "separator": [{ + "value": ",", + "tools": ["IDMassAccuracy"] + }], + + "#": "don't alow to copy data internally to save computation time for reloading", + "copy_data": [{ + "value": "false", + "tools": ["MapAlignerTreeGuided"] + }], + + "#": "overwrite/add Galaxy xml attributes of some parameters (names need to start with param_)", + + "#": "test is not a hardcoded value since we need to set it in the tool tests", + "test": [{ + "CTD:type": "text", + "XML:type": "hidden" + }], + + "#": "overwrite CTD attributes of some parameters (some are not possible, e.g. type)", + + "#": "for some tools the user needs to select the desired output type since detection by extension makes no sense for galaxy tools", + "out_type": [{ + "CTD:required": true, + "CTD:advanced": false + }], + + "#": "SeedListGenerator with consensusXML input needs a dynamic number of outputs that depends on the content of the input, so we remove this options at the moment because its hard or impossible to implement in Galaxy, https://github.com/OpenMS/OpenMS/issues/4404 .. see also in parameter", + "#": "FileInfo, MapStatistics, SequenceCoverageCalculator wo -out just writes to stdout. not wanted here", + "#": "MzMLSplitter output prefix https://github.com/OpenMS/OpenMS/issues/4404", + "#": "IDRipper: blacklist out (is doing the same as the output-prefix out-path)", + "out": [{ + "CTD:is_list": false, + "tools": ["SeedListGenerator"] + }, { + "CTD:required": true, + "tools": ["FileInfo", "MapStatistics", "SequenceCoverageCalculator"] + }, { + "CTD:type": "output-prefix", + "CTD:required": true, + "CTD:restrictions": "mzml", + "tools": ["MzMLSplitter"] + }, { + "value": "@", + "tools": ["IDRipper"] + }], + + "#": "Try to remove xml data type whereever possible", + "#": "XTandem Adapter output is called .xml in OMS which is to unspecific -> use Galaxy's bioml", + "xml_out": [{ + "CTD:restrictions": "bioml", + "tools": ["XTandemAdapter"] + }], + + "#": "IDFileConverter remove xml", + "#": "OpenSwathWorkflow make in single file input and all outputs non-optional", + "#": "XFDR does not need xml .. redundant with xquest.xml TODO check if list is up to date with each new release", + "#": "SeedListGenerator: remove consensusXML https://github.com/OpenMS/OpenMS/issues/4404 .. see also out parameter", + "in": [{ + "CTD:restrictions": "pepXML,protXML,mascotXML,omssaXML,bioml,psms,tsv,idXML,mzid,xquest.xml", + "tools": ["IDFileConverter"] + }, { + "CTD:is_list": false, + "tools": ["OpenSwathWorkflow"] + }, { + "CTD:restrictions": "idXML,mzid,xquest.xml", + "tools": ["XFDR"] + }, { + "CTD:restrictions": "mzML,idXML,featureXML", + "tools": ["SeedListGenerator"] + }], + + "#": "IDMapper has in and spectra:in params, in is used in out as format_source", + "#": "which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493", + "spectra:in": [{ + "CTD:name": "_in", + "tools": ["IDMapper"] + }], + + "#": "hardcoding prefix parameters which are not yet available in OMS but in CTDOpts https://github.com/OpenMS/OpenMS/pull/4527", + "#": "output-prefix", + "out_path": [{ + "CTD:type": "output-prefix", + "CTD:required": true, + "CTD:restrictions": "idXML", + "tools": ["IDRipper"] + }], + "outputDirectory": [{ + "CTD:type": "output-prefix", + "CTD:advanced": false, + "CTD:required": true, + "CTD:restrictions": "mzml", + "tools": ["OpenSwathFileSplitter"] + }], + + "#": "OpenSwathDIAPreScoring: https://github.com/OpenMS/OpenMS/pull/4443", + "#": "SpectraSTSearchAdapter does not need xml .. redundant with pep.xml TODO check if list is up to date with each new release", + "output_files": [{ + "CTD:required": true, + "tools": ["OpenSwathDIAPreScoring"] + }, { + "CTD:restrictions": "txt,tsv,pep.xml,pepXML,html", + "tools": ["SpectraSTSearchAdapter"] + + }] +}
--- a/macros.xml Fri May 17 10:22:48 2019 -0400 +++ b/macros.xml Tue Oct 13 19:52:20 2020 +0000 @@ -1,11 +1,20 @@ <?xml version='1.0' encoding='UTF-8'?> +<!-- CTD2Galaxy depends on this file and on the stdio, advanced_options macros! + You can edit this file to add your own macros, if you so desire, or you can + add additional macro files using the m/macros parameter --> <macros> + <token name="@TOOL_VERSION@">2.6</token> + <token name="@GALAXY_VERSION@">0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="2.3">openms</requirement> - <requirement type="package" version="15.12.15.2">xtandem</requirement> - <requirement type="package" version="1.0">fido</requirement> - <requirement type="package" version="2017.07.21">msgf_plus</requirement> + <requirement type="package" version="@TOOL_VERSION@">openms</requirement> + <requirement type="package" version="@TOOL_VERSION@">openms-thirdparty</requirement> + <!-- makeblastdb for OMSSAAdapter --> + <requirement type="package" version="2.9.0">blast</requirement> + <!--<requirement type="package" version="5.0.0">tpp</requirement>--> + <!-- for realpath (used e.g. in LuciphorAdapter) --> + <!--<requirement type="package" version="8.25">coreutils</requirement>--> + <requirement type="package" version="1.4">ctdopts</requirement> <yield/> </requirements> </xml> @@ -21,8 +30,8 @@ <citation type="doi">doi:10.1186/1471-2105-9-163</citation> </citations> </xml> - <xml name="advanced_options"> - <conditional name="adv_opts"> + <xml name="adv_opts_macro"> + <conditional name="adv_opts_cond"> <param name="adv_opts_selector" type="select" label="Advanced Options"> <option value="basic" selected="True">Hide Advanced Options</option> <option value="advanced">Show Advanced Options</option> @@ -33,4 +42,87 @@ </when> </conditional> </xml> -</macros> + + <!-- sanitizers and validators --> + <xml name="list_string_val"> + <validator type="regex" message="parameter must not start with $">^[^$]</validator> + + <validator type="regex" message="a space separated list of string is needed (strings that contain spaces can be quoted with ")">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator> + </xml> + <xml name="list_string_san"> + <sanitizer> + <valid initial="string.printable"> +<!-- <remove value="'"/>--> +<!-- <remove value="\"/>--><!-- otherwise the user could quote the final quote --> +<!-- <remove value="`"/>--> +<!-- <remove value="$"/>--> +<!-- <remove value="<"/>--> + <!--<remove value="&"/> removed for MascotAdapterOnline -Mascot_server:export_params which is a URL POST string which can contain & .. could be mapped to & but there is still a & --> + <!--<remove value=";"/>--> +<!-- <remove value="#"/>--> + </valid> + </sanitizer> + </xml> + <xml name="list_float_valsan"> + <validator type="regex" message="a space separated list of float values is required">^ *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?( *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* *$</validator> + <yield/> + <sanitizer> + <valid initial="string.digits"> + <add value=" "/> + <add value="."/> + <add value="E"/> + <add value="e"/> + <add value="+"/> + <add value="-"/> + </valid> + </sanitizer> + </xml> + <xml name="list_integer_valsan"> + <validator type="regex" message="a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator> + <yield/> + <sanitizer> + <valid initial="string.digits"> + <add value=" "/> + <add value="+"/> + <add value="-"/> + </valid> + </sanitizer> + </xml> + + <!-- helper function to quote space separated strings --> + <token name="@QUOTE_FOO@"> +#def quote(s): + #set $s = [ _ for _ in $s.split(" ") if _ != "" ] + #set $q = False + #for $i, $p in enumerate($s): + #if $p == "": + #continue + #end if + #if $p.startswith('"'): + #set $q = True + #end if +## #if p.startswith('-'): +## #set p = "\\" + p +## #elif p.startswith('"-'): +## #set p = "\\" + p[1:] +## #end if + #if not $q: + #set $s[i] = '"%s"' % p + #end if + #if $p.endswith('"'): + #set $q = False + #end if + #end for + #return " ".join($s) +#end def + </token> + +<token name="@EXT_FOO@"><![CDATA[#def oms2gxyext(o) + #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'} + #return m[o] +#end def +#def gxy2omsext(g) + #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'} + #return m[g] +#end def +]]></token></macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_autotest.xml Tue Oct 13 19:52:20 2020 +0000 @@ -0,0 +1,27205 @@ +<?xml version='1.0' encoding='UTF-8'?> +<macros> + <xml name="autotest_AccurateMassSearch"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/> + <output name="out" file="AccurateMassSearch_1_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> + <param name="positive_adducts" value="CHEMISTRY/PositiveAdducts.tsv" ftype="tabular"/> + <param name="negative_adducts" value="CHEMISTRY/NegativeAdducts.tsv" ftype="tabular"/> + <section name="db"> + <param name="mapping" value="CHEMISTRY/HMDBMappingFile.tsv" ftype="tabular"/> + <param name="struct" value="CHEMISTRY/HMDB2StructMapping.tsv" ftype="tabular"/> + </section> + <section name="algorithm"> + <param name="mass_error_value" value="5.0"/> + <param name="mass_error_unit" value="ppm"/> + <param name="ionization_mode" value="positive"/> + <param name="isotopic_similarity" value="false"/> + <param name="use_feature_adducts" value="false"/> + <param name="keep_unidentified_masses" value="false"/> + <section name="mzTab"> + <param name="exportIsotopeIntensities" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="AccurateMassSearch_2_input.featureXML"/> + <output name="out" file="AccurateMassSearch_2_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> + <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/> + <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/> + <section name="db"> + <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/> + <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/> + </section> + <section name="algorithm"> + <param name="mass_error_value" value="5.0"/> + <param name="mass_error_unit" value="ppm"/> + <param name="ionization_mode" value="positive"/> + <param name="isotopic_similarity" value="false"/> + <param name="use_feature_adducts" value="false"/> + <param name="keep_unidentified_masses" value="false"/> + <section name="mzTab"> + <param name="exportIsotopeIntensities" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="AccurateMassSearch_2_input.featureXML"/> + <output name="out" file="AccurateMassSearch_3_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> + <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/> + <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/> + <section name="db"> + <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/> + <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/> + </section> + <section name="algorithm"> + <param name="mass_error_value" value="5.0"/> + <param name="mass_error_unit" value="ppm"/> + <param name="ionization_mode" value="positive"/> + <param name="isotopic_similarity" value="false"/> + <param name="use_feature_adducts" value="false"/> + <param name="keep_unidentified_masses" value="false"/> + <section name="mzTab"> + <param name="exportIsotopeIntensities" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_AssayGeneratorMetabo"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="precursor_recalibration_window" value="0.1"/> + <param name="precursor_recalibration_window_unit" value="Da"/> + <param name="min_fragment_mz" value="0.0"/> + <param name="max_fragment_mz" value="2000.0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="AssayGeneratorMetabo_input.mzML"/> + <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/> + <param name="out_type" value="tsv"/> + <output name="out" file="AssayGeneratorMetabo_ffm_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="fragment_annotation" value="none"/> + <param name="method" value="highest_intensity"/> + <param name="use_exact_mass" value="false"/> + <param name="exclude_ms2_precursor" value="false"/> + <param name="precursor_mz_distance" value="0.0001"/> + <param name="precursor_rt_tolerance" value="5.0"/> + <param name="use_known_unknowns" value="false"/> + <param name="min_transitions" value="1"/> + <param name="max_transitions" value="3"/> + <param name="cosine_similarity_threshold" value="0.98"/> + <param name="transition_threshold" value="5.0"/> + <param name="out_workspace_directory" value=""/> + <section name="deisotoping"> + <param name="use_deisotoper" value="false"/> + <param name="fragment_tolerance" value="1.0"/> + <param name="fragment_unit" value="ppm"/> + <param name="min_charge" value="1"/> + <param name="max_charge" value="1"/> + <param name="min_isopeaks" value="2"/> + <param name="max_isopeaks" value="3"/> + <param name="keep_only_deisotoped" value="false"/> + <param name="annotate_charge" value="false"/> + </section> + <section name="preprocessing"> + <param name="filter_by_num_masstraces" value="1"/> + <param name="precursor_mz_tolerance" value="0.005"/> + <param name="precursor_mz_tolerance_unit" value="Da"/> + <param name="precursor_rt_tolerance" value="5"/> + <param name="isotope_pattern_iterations" value="3"/> + <param name="feature_only" value="false"/> + <param name="no_masstrace_info_isotope_pattern" value="false"/> + </section> + <section name="sirius"> + <param name="profile" value="qtof"/> + <param name="candidates" value="5"/> + <param name="database" value="all"/> + <param name="noise" value="0"/> + <param name="ppm_max" value="10"/> + <param name="isotope" value="both"/> + <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> + <param name="compound_timeout" value="10"/> + <param name="tree_timeout" value="0"/> + <param name="top_n_hits" value="10"/> + <param name="auto_charge" value="false"/> + <param name="ion_tree" value="false"/> + <param name="no_recalibration" value="false"/> + <param name="most_intense_ms2" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="precursor_recalibration_window" value="0.1"/> + <param name="precursor_recalibration_window_unit" value="Da"/> + <param name="min_fragment_mz" value="0.0"/> + <param name="max_fragment_mz" value="2000.0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="AssayGeneratorMetabo_input.mzML"/> + <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> + <param name="out_type" value="tsv"/> + <output name="out" file="AssayGeneratorMetabo_ams_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="fragment_annotation" value="none"/> + <param name="method" value="highest_intensity"/> + <param name="use_exact_mass" value="false"/> + <param name="exclude_ms2_precursor" value="false"/> + <param name="precursor_mz_distance" value="0.0001"/> + <param name="precursor_rt_tolerance" value="5.0"/> + <param name="use_known_unknowns" value="false"/> + <param name="min_transitions" value="1"/> + <param name="max_transitions" value="3"/> + <param name="cosine_similarity_threshold" value="0.98"/> + <param name="transition_threshold" value="5.0"/> + <param name="out_workspace_directory" value=""/> + <section name="deisotoping"> + <param name="use_deisotoper" value="false"/> + <param name="fragment_tolerance" value="1.0"/> + <param name="fragment_unit" value="ppm"/> + <param name="min_charge" value="1"/> + <param name="max_charge" value="1"/> + <param name="min_isopeaks" value="2"/> + <param name="max_isopeaks" value="3"/> + <param name="keep_only_deisotoped" value="false"/> + <param name="annotate_charge" value="false"/> + </section> + <section name="preprocessing"> + <param name="filter_by_num_masstraces" value="1"/> + <param name="precursor_mz_tolerance" value="0.005"/> + <param name="precursor_mz_tolerance_unit" value="Da"/> + <param name="precursor_rt_tolerance" value="5"/> + <param name="isotope_pattern_iterations" value="3"/> + <param name="feature_only" value="false"/> + <param name="no_masstrace_info_isotope_pattern" value="false"/> + </section> + <section name="sirius"> + <param name="profile" value="qtof"/> + <param name="candidates" value="5"/> + <param name="database" value="all"/> + <param name="noise" value="0"/> + <param name="ppm_max" value="10"/> + <param name="isotope" value="both"/> + <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> + <param name="compound_timeout" value="10"/> + <param name="tree_timeout" value="0"/> + <param name="top_n_hits" value="10"/> + <param name="auto_charge" value="false"/> + <param name="ion_tree" value="false"/> + <param name="no_recalibration" value="false"/> + <param name="most_intense_ms2" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="precursor_recalibration_window" value="0.1"/> + <param name="precursor_recalibration_window_unit" value="Da"/> + <param name="min_fragment_mz" value="0.0"/> + <param name="max_fragment_mz" value="2000.0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="AssayGeneratorMetabo_input.mzML"/> + <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/> + <param name="out_type" value="tsv"/> + <output name="out" file="AssayGeneratorMetabo_ffm_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="fragment_annotation" value="none"/> + <param name="method" value="consensus_spectrum"/> + <param name="use_exact_mass" value="false"/> + <param name="exclude_ms2_precursor" value="false"/> + <param name="precursor_mz_distance" value="0.0001"/> + <param name="precursor_rt_tolerance" value="5.0"/> + <param name="use_known_unknowns" value="false"/> + <param name="min_transitions" value="1"/> + <param name="max_transitions" value="3"/> + <param name="cosine_similarity_threshold" value="0.98"/> + <param name="transition_threshold" value="5.0"/> + <param name="out_workspace_directory" value=""/> + <section name="deisotoping"> + <param name="use_deisotoper" value="false"/> + <param name="fragment_tolerance" value="1.0"/> + <param name="fragment_unit" value="ppm"/> + <param name="min_charge" value="1"/> + <param name="max_charge" value="1"/> + <param name="min_isopeaks" value="2"/> + <param name="max_isopeaks" value="3"/> + <param name="keep_only_deisotoped" value="false"/> + <param name="annotate_charge" value="false"/> + </section> + <section name="preprocessing"> + <param name="filter_by_num_masstraces" value="1"/> + <param name="precursor_mz_tolerance" value="0.005"/> + <param name="precursor_mz_tolerance_unit" value="Da"/> + <param name="precursor_rt_tolerance" value="5"/> + <param name="isotope_pattern_iterations" value="3"/> + <param name="feature_only" value="false"/> + <param name="no_masstrace_info_isotope_pattern" value="false"/> + </section> + <section name="sirius"> + <param name="profile" value="qtof"/> + <param name="candidates" value="5"/> + <param name="database" value="all"/> + <param name="noise" value="0"/> + <param name="ppm_max" value="10"/> + <param name="isotope" value="both"/> + <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> + <param name="compound_timeout" value="10"/> + <param name="tree_timeout" value="0"/> + <param name="top_n_hits" value="10"/> + <param name="auto_charge" value="false"/> + <param name="ion_tree" value="false"/> + <param name="no_recalibration" value="false"/> + <param name="most_intense_ms2" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="precursor_recalibration_window" value="0.1"/> + <param name="precursor_recalibration_window_unit" value="Da"/> + <param name="min_fragment_mz" value="0.0"/> + <param name="max_fragment_mz" value="2000.0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="AssayGeneratorMetabo_input.mzML"/> + <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> + <param name="out_type" value="tsv"/> + <output name="out" file="AssayGeneratorMetabo_ams_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="fragment_annotation" value="none"/> + <param name="method" value="consensus_spectrum"/> + <param name="use_exact_mass" value="false"/> + <param name="exclude_ms2_precursor" value="false"/> + <param name="precursor_mz_distance" value="0.0001"/> + <param name="precursor_rt_tolerance" value="5.0"/> + <param name="use_known_unknowns" value="false"/> + <param name="min_transitions" value="1"/> + <param name="max_transitions" value="3"/> + <param name="cosine_similarity_threshold" value="0.98"/> + <param name="transition_threshold" value="5.0"/> + <param name="out_workspace_directory" value=""/> + <section name="deisotoping"> + <param name="use_deisotoper" value="false"/> + <param name="fragment_tolerance" value="1.0"/> + <param name="fragment_unit" value="ppm"/> + <param name="min_charge" value="1"/> + <param name="max_charge" value="1"/> + <param name="min_isopeaks" value="2"/> + <param name="max_isopeaks" value="3"/> + <param name="keep_only_deisotoped" value="false"/> + <param name="annotate_charge" value="false"/> + </section> + <section name="preprocessing"> + <param name="filter_by_num_masstraces" value="1"/> + <param name="precursor_mz_tolerance" value="0.005"/> + <param name="precursor_mz_tolerance_unit" value="Da"/> + <param name="precursor_rt_tolerance" value="5"/> + <param name="isotope_pattern_iterations" value="3"/> + <param name="feature_only" value="false"/> + <param name="no_masstrace_info_isotope_pattern" value="false"/> + </section> + <section name="sirius"> + <param name="profile" value="qtof"/> + <param name="candidates" value="5"/> + <param name="database" value="all"/> + <param name="noise" value="0"/> + <param name="ppm_max" value="10"/> + <param name="isotope" value="both"/> + <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> + <param name="compound_timeout" value="10"/> + <param name="tree_timeout" value="0"/> + <param name="top_n_hits" value="10"/> + <param name="auto_charge" value="false"/> + <param name="ion_tree" value="false"/> + <param name="no_recalibration" value="false"/> + <param name="most_intense_ms2" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="precursor_recalibration_window" value="0.1"/> + <param name="precursor_recalibration_window_unit" value="Da"/> + <param name="min_fragment_mz" value="0.0"/> + <param name="max_fragment_mz" value="2000.0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="AssayGeneratorMetabo_input.mzML"/> + <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> + <param name="out_type" value="tsv"/> + <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="fragment_annotation" value="none"/> + <param name="method" value="consensus_spectrum"/> + <param name="use_exact_mass" value="false"/> + <param name="exclude_ms2_precursor" value="false"/> + <param name="precursor_mz_distance" value="0.0001"/> + <param name="precursor_rt_tolerance" value="5.0"/> + <param name="use_known_unknowns" value="true"/> + <param name="min_transitions" value="1"/> + <param name="max_transitions" value="3"/> + <param name="cosine_similarity_threshold" value="0.98"/> + <param name="transition_threshold" value="5.0"/> + <param name="out_workspace_directory" value=""/> + <section name="deisotoping"> + <param name="use_deisotoper" value="false"/> + <param name="fragment_tolerance" value="1.0"/> + <param name="fragment_unit" value="ppm"/> + <param name="min_charge" value="1"/> + <param name="max_charge" value="1"/> + <param name="min_isopeaks" value="2"/> + <param name="max_isopeaks" value="3"/> + <param name="keep_only_deisotoped" value="false"/> + <param name="annotate_charge" value="false"/> + </section> + <section name="preprocessing"> + <param name="filter_by_num_masstraces" value="1"/> + <param name="precursor_mz_tolerance" value="0.005"/> + <param name="precursor_mz_tolerance_unit" value="Da"/> + <param name="precursor_rt_tolerance" value="5"/> + <param name="isotope_pattern_iterations" value="3"/> + <param name="feature_only" value="false"/> + <param name="no_masstrace_info_isotope_pattern" value="false"/> + </section> + <section name="sirius"> + <param name="profile" value="qtof"/> + <param name="candidates" value="5"/> + <param name="database" value="all"/> + <param name="noise" value="0"/> + <param name="ppm_max" value="10"/> + <param name="isotope" value="both"/> + <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> + <param name="compound_timeout" value="10"/> + <param name="tree_timeout" value="0"/> + <param name="top_n_hits" value="10"/> + <param name="auto_charge" value="false"/> + <param name="ion_tree" value="false"/> + <param name="no_recalibration" value="false"/> + <param name="most_intense_ms2" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="precursor_recalibration_window" value="0.1"/> + <param name="precursor_recalibration_window_unit" value="Da"/> + <param name="min_fragment_mz" value="0.0"/> + <param name="max_fragment_mz" value="2000.0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="AssayGeneratorMetabo_input.mzML"/> + <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> + <param name="out_type" value="tsv"/> + <output name="out" file="AssayGeneratorMetabo_ams_sirius_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="fragment_annotation" value="sirius"/> + <param name="method" value="highest_intensity"/> + <param name="use_exact_mass" value="true"/> + <param name="exclude_ms2_precursor" value="false"/> + <param name="precursor_mz_distance" value="0.0001"/> + <param name="precursor_rt_tolerance" value="5.0"/> + <param name="use_known_unknowns" value="false"/> + <param name="min_transitions" value="2"/> + <param name="max_transitions" value="3"/> + <param name="cosine_similarity_threshold" value="0.98"/> + <param name="transition_threshold" value="3.0"/> + <param name="out_workspace_directory" value=""/> + <section name="deisotoping"> + <param name="use_deisotoper" value="false"/> + <param name="fragment_tolerance" value="1.0"/> + <param name="fragment_unit" value="ppm"/> + <param name="min_charge" value="1"/> + <param name="max_charge" value="1"/> + <param name="min_isopeaks" value="2"/> + <param name="max_isopeaks" value="3"/> + <param name="keep_only_deisotoped" value="false"/> + <param name="annotate_charge" value="false"/> + </section> + <section name="preprocessing"> + <param name="filter_by_num_masstraces" value="1"/> + <param name="precursor_mz_tolerance" value="10.0"/> + <param name="precursor_mz_tolerance_unit" value="ppm"/> + <param name="precursor_rt_tolerance" value="5"/> + <param name="isotope_pattern_iterations" value="3"/> + <param name="feature_only" value="true"/> + <param name="no_masstrace_info_isotope_pattern" value="false"/> + </section> + <section name="sirius"> + <param name="profile" value="qtof"/> + <param name="candidates" value="5"/> + <param name="database" value="all"/> + <param name="noise" value="0"/> + <param name="ppm_max" value="10"/> + <param name="isotope" value="both"/> + <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> + <param name="compound_timeout" value="100"/> + <param name="tree_timeout" value="0"/> + <param name="top_n_hits" value="10"/> + <param name="auto_charge" value="false"/> + <param name="ion_tree" value="false"/> + <param name="no_recalibration" value="false"/> + <param name="most_intense_ms2" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="precursor_recalibration_window" value="0.1"/> + <param name="precursor_recalibration_window_unit" value="Da"/> + <param name="min_fragment_mz" value="0.0"/> + <param name="max_fragment_mz" value="2000.0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="AssayGeneratorMetabo_input.mzML"/> + <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> + <param name="out_type" value="tsv"/> + <output name="out" file="AssayGeneratorMetabo_ams_sirius_ukn_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="fragment_annotation" value="sirius"/> + <param name="method" value="highest_intensity"/> + <param name="use_exact_mass" value="true"/> + <param name="exclude_ms2_precursor" value="false"/> + <param name="precursor_mz_distance" value="0.0001"/> + <param name="precursor_rt_tolerance" value="5.0"/> + <param name="use_known_unknowns" value="true"/> + <param name="min_transitions" value="2"/> + <param name="max_transitions" value="3"/> + <param name="cosine_similarity_threshold" value="0.98"/> + <param name="transition_threshold" value="3.0"/> + <param name="out_workspace_directory" value=""/> + <section name="deisotoping"> + <param name="use_deisotoper" value="false"/> + <param name="fragment_tolerance" value="1.0"/> + <param name="fragment_unit" value="ppm"/> + <param name="min_charge" value="1"/> + <param name="max_charge" value="1"/> + <param name="min_isopeaks" value="2"/> + <param name="max_isopeaks" value="3"/> + <param name="keep_only_deisotoped" value="false"/> + <param name="annotate_charge" value="false"/> + </section> + <section name="preprocessing"> + <param name="filter_by_num_masstraces" value="1"/> + <param name="precursor_mz_tolerance" value="10.0"/> + <param name="precursor_mz_tolerance_unit" value="ppm"/> + <param name="precursor_rt_tolerance" value="5"/> + <param name="isotope_pattern_iterations" value="3"/> + <param name="feature_only" value="true"/> + <param name="no_masstrace_info_isotope_pattern" value="false"/> + </section> + <section name="sirius"> + <param name="profile" value="qtof"/> + <param name="candidates" value="5"/> + <param name="database" value="all"/> + <param name="noise" value="0"/> + <param name="ppm_max" value="10"/> + <param name="isotope" value="both"/> + <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> + <param name="compound_timeout" value="100"/> + <param name="tree_timeout" value="0"/> + <param name="top_n_hits" value="10"/> + <param name="auto_charge" value="false"/> + <param name="ion_tree" value="false"/> + <param name="no_recalibration" value="false"/> + <param name="most_intense_ms2" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="precursor_recalibration_window" value="0.1"/> + <param name="precursor_recalibration_window_unit" value="Da"/> + <param name="min_fragment_mz" value="0.0"/> + <param name="max_fragment_mz" value="2000.0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="AssayGeneratorMetabo_intsort_input.mzML"/> + <param name="in_id" value="AssayGeneratorMetabo_intsort_input.featureXML"/> + <param name="out_type" value="tsv"/> + <output name="out" file="AssayGeneratorMetabo_ams_sirius_intsort_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="fragment_annotation" value="sirius"/> + <param name="method" value="highest_intensity"/> + <param name="use_exact_mass" value="true"/> + <param name="exclude_ms2_precursor" value="false"/> + <param name="precursor_mz_distance" value="0.0001"/> + <param name="precursor_rt_tolerance" value="5.0"/> + <param name="use_known_unknowns" value="false"/> + <param name="min_transitions" value="2"/> + <param name="max_transitions" value="3"/> + <param name="cosine_similarity_threshold" value="0.98"/> + <param name="transition_threshold" value="3.0"/> + <param name="out_workspace_directory" value=""/> + <section name="deisotoping"> + <param name="use_deisotoper" value="false"/> + <param name="fragment_tolerance" value="1.0"/> + <param name="fragment_unit" value="ppm"/> + <param name="min_charge" value="1"/> + <param name="max_charge" value="1"/> + <param name="min_isopeaks" value="2"/> + <param name="max_isopeaks" value="3"/> + <param name="keep_only_deisotoped" value="false"/> + <param name="annotate_charge" value="false"/> + </section> + <section name="preprocessing"> + <param name="filter_by_num_masstraces" value="1"/> + <param name="precursor_mz_tolerance" value="10.0"/> + <param name="precursor_mz_tolerance_unit" value="ppm"/> + <param name="precursor_rt_tolerance" value="5"/> + <param name="isotope_pattern_iterations" value="3"/> + <param name="feature_only" value="true"/> + <param name="no_masstrace_info_isotope_pattern" value="false"/> + </section> + <section name="sirius"> + <param name="profile" value="qtof"/> + <param name="candidates" value="5"/> + <param name="database" value="all"/> + <param name="noise" value="0"/> + <param name="ppm_max" value="10"/> + <param name="isotope" value="both"/> + <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> + <param name="compound_timeout" value="100"/> + <param name="tree_timeout" value="0"/> + <param name="top_n_hits" value="10"/> + <param name="auto_charge" value="false"/> + <param name="ion_tree" value="false"/> + <param name="no_recalibration" value="false"/> + <param name="most_intense_ms2" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="precursor_recalibration_window" value="0.1"/> + <param name="precursor_recalibration_window_unit" value="Da"/> + <param name="min_fragment_mz" value="100.0"/> + <param name="max_fragment_mz" value="900.0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="AssayGeneratorMetabo_input.mzML"/> + <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> + <param name="out_type" value="tsv"/> + <output name="out" file="AssayGeneratorMetabo_ams_sirius_restrict_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="fragment_annotation" value="sirius"/> + <param name="method" value="highest_intensity"/> + <param name="use_exact_mass" value="true"/> + <param name="exclude_ms2_precursor" value="false"/> + <param name="precursor_mz_distance" value="0.0001"/> + <param name="precursor_rt_tolerance" value="5.0"/> + <param name="use_known_unknowns" value="false"/> + <param name="min_transitions" value="2"/> + <param name="max_transitions" value="3"/> + <param name="cosine_similarity_threshold" value="0.98"/> + <param name="transition_threshold" value="3.0"/> + <param name="out_workspace_directory" value=""/> + <section name="deisotoping"> + <param name="use_deisotoper" value="false"/> + <param name="fragment_tolerance" value="1.0"/> + <param name="fragment_unit" value="ppm"/> + <param name="min_charge" value="1"/> + <param name="max_charge" value="1"/> + <param name="min_isopeaks" value="2"/> + <param name="max_isopeaks" value="3"/> + <param name="keep_only_deisotoped" value="false"/> + <param name="annotate_charge" value="false"/> + </section> + <section name="preprocessing"> + <param name="filter_by_num_masstraces" value="1"/> + <param name="precursor_mz_tolerance" value="10.0"/> + <param name="precursor_mz_tolerance_unit" value="ppm"/> + <param name="precursor_rt_tolerance" value="5"/> + <param name="isotope_pattern_iterations" value="3"/> + <param name="feature_only" value="true"/> + <param name="no_masstrace_info_isotope_pattern" value="false"/> + </section> + <section name="sirius"> + <param name="profile" value="qtof"/> + <param name="candidates" value="5"/> + <param name="database" value="all"/> + <param name="noise" value="0"/> + <param name="ppm_max" value="10"/> + <param name="isotope" value="both"/> + <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> + <param name="compound_timeout" value="100"/> + <param name="tree_timeout" value="0"/> + <param name="top_n_hits" value="10"/> + <param name="auto_charge" value="false"/> + <param name="ion_tree" value="false"/> + <param name="no_recalibration" value="false"/> + <param name="most_intense_ms2" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_BaselineFilter"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="BaselineFilter_input.mzML"/> + <output name="out" file="BaselineFilter_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="struc_elem_length" value="1.5"/> + <param name="struc_elem_unit" value="Thomson"/> + <param name="method" value="tophat"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_ClusterMassTracesByPrecursor"> +</xml> + <xml name="autotest_ClusterMassTraces"> +</xml> + <xml name="autotest_CometAdapter"> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="use_A_ions" value="false"/> + <param name="use_B_ions" value="true"/> + <param name="use_C_ions" value="false"/> + <param name="use_X_ions" value="false"/> + <param name="use_Y_ions" value="true"/> + <param name="use_Z_ions" value="false"/> + <param name="use_NL_ions" value="false"/> + <param name="second_enzyme" value=""/> + <param name="digest_mass_range" value="600:5000"/> + <param name="max_precursor_charge" value="5"/> + <param name="spectrum_batch_size" value="1000"/> + <param name="mass_offsets" value="0.0"/> + <param name="minimum_peaks" value="10"/> + <param name="minimum_intensity" value="0.0"/> + <param name="remove_precursor_peak" value="no"/> + <param name="remove_precursor_tolerance" value="1.5"/> + <param name="clear_mz_range" value="0:0"/> + <param name="max_variable_mods_in_peptide" value="5"/> + <param name="require_variable_mod" value="false"/> + <param name="force" value="true"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="spectra_comet.mzML"/> + <output name="out" file="CometAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="database" value="proteins.fasta"/> + <output name="pin_out" file="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="precursor_mass_tolerance" value="3.0"/> + <param name="precursor_error_units" value="ppm"/> + <param name="isotope_error" value="off"/> + <param name="fragment_mass_tolerance" value="0.50025"/> + <param name="fragment_error_units" value="Da"/> + <param name="fragment_bin_offset" value="0.25"/> + <param name="instrument" value="high_res"/> + <param name="enzyme" value="Trypsin"/> + <param name="num_enzyme_termini" value="fully"/> + <param name="missed_cleavages" value="1"/> + <param name="min_peptide_length" value="5"/> + <param name="max_peptide_length" value="63"/> + <param name="num_hits" value="5"/> + <param name="precursor_charge" value="0:0"/> + <param name="override_charge" value="keep any known"/> + <param name="ms_level" value="2"/> + <param name="activation_method" value="ALL"/> + <param name="max_fragment_charge" value="3"/> + <param name="clip_nterm_methionine" value="false"/> + <param name="fixed_modifications" value=""/> + <param name="variable_modifications" value=""/> + <param name="binary_modifications" value=""/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="use_A_ions" value="false"/> + <param name="use_B_ions" value="true"/> + <param name="use_C_ions" value="false"/> + <param name="use_X_ions" value="false"/> + <param name="use_Y_ions" value="true"/> + <param name="use_Z_ions" value="false"/> + <param name="use_NL_ions" value="false"/> + <param name="second_enzyme" value=""/> + <param name="digest_mass_range" value="600:5000"/> + <param name="max_precursor_charge" value="5"/> + <param name="spectrum_batch_size" value="1000"/> + <param name="mass_offsets" value="0.0"/> + <param name="minimum_peaks" value="10"/> + <param name="minimum_intensity" value="0.0"/> + <param name="remove_precursor_peak" value="no"/> + <param name="remove_precursor_tolerance" value="1.5"/> + <param name="clear_mz_range" value="0:0"/> + <param name="max_variable_mods_in_peptide" value="5"/> + <param name="require_variable_mod" value="false"/> + <param name="force" value="true"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="CometAdapter_2_prepared.mzML"/> + <output name="out" file="CometAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="database" value="CometAdapter_2_in.fasta"/> + <output name="pin_out" file="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="precursor_mass_tolerance" value="3.0"/> + <param name="precursor_error_units" value="Da"/> + <param name="isotope_error" value="off"/> + <param name="fragment_mass_tolerance" value="0.50025"/> + <param name="fragment_error_units" value="Da"/> + <param name="fragment_bin_offset" value="0.25"/> + <param name="instrument" value="high_res"/> + <param name="enzyme" value="Trypsin"/> + <param name="num_enzyme_termini" value="fully"/> + <param name="missed_cleavages" value="1"/> + <param name="min_peptide_length" value="5"/> + <param name="max_peptide_length" value="63"/> + <param name="num_hits" value="5"/> + <param name="precursor_charge" value="0:0"/> + <param name="override_charge" value="keep any known"/> + <param name="ms_level" value="2"/> + <param name="activation_method" value="ALL"/> + <param name="max_fragment_charge" value="3"/> + <param name="clip_nterm_methionine" value="false"/> + <param name="fixed_modifications" value=""/> + <param name="variable_modifications" value=""/> + <param name="binary_modifications" value=""/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="use_A_ions" value="false"/> + <param name="use_B_ions" value="true"/> + <param name="use_C_ions" value="false"/> + <param name="use_X_ions" value="false"/> + <param name="use_Y_ions" value="true"/> + <param name="use_Z_ions" value="false"/> + <param name="use_NL_ions" value="false"/> + <param name="second_enzyme" value=""/> + <param name="digest_mass_range" value="600:5000"/> + <param name="max_precursor_charge" value="5"/> + <param name="spectrum_batch_size" value="20000"/> + <param name="mass_offsets" value="0.0"/> + <param name="minimum_peaks" value="10"/> + <param name="minimum_intensity" value="0.0"/> + <param name="remove_precursor_peak" value="no"/> + <param name="remove_precursor_tolerance" value="1.5"/> + <param name="clear_mz_range" value="0:0"/> + <param name="max_variable_mods_in_peptide" value="3"/> + <param name="require_variable_mod" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="CometAdapter_3.mzML"/> + <output name="out" file="CometAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="database" value="CometAdapter_3.fasta"/> + <output name="pin_out" file="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="precursor_mass_tolerance" value="5.0"/> + <param name="precursor_error_units" value="ppm"/> + <param name="isotope_error" value="off"/> + <param name="fragment_mass_tolerance" value="0.01"/> + <param name="fragment_error_units" value="Da"/> + <param name="fragment_bin_offset" value="0.0"/> + <param name="instrument" value="high_res"/> + <param name="enzyme" value="Trypsin"/> + <param name="num_enzyme_termini" value="fully"/> + <param name="missed_cleavages" value="3"/> + <param name="min_peptide_length" value="5"/> + <param name="max_peptide_length" value="63"/> + <param name="num_hits" value="5"/> + <param name="precursor_charge" value="0:0"/> + <param name="override_charge" value="keep known search unknown"/> + <param name="ms_level" value="2"/> + <param name="activation_method" value="ALL"/> + <param name="max_fragment_charge" value="3"/> + <param name="clip_nterm_methionine" value="false"/> + <param name="fixed_modifications" value="Carbamidomethyl (C)"/> + <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term)"/> + <param name="binary_modifications" value=""/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="use_A_ions" value="false"/> + <param name="use_B_ions" value="true"/> + <param name="use_C_ions" value="false"/> + <param name="use_X_ions" value="false"/> + <param name="use_Y_ions" value="true"/> + <param name="use_Z_ions" value="false"/> + <param name="use_NL_ions" value="false"/> + <param name="second_enzyme" value=""/> + <param name="digest_mass_range" value="600:1200"/> + <param name="max_precursor_charge" value="5"/> + <param name="spectrum_batch_size" value="20000"/> + <param name="mass_offsets" value="0.0"/> + <param name="minimum_peaks" value="10"/> + <param name="minimum_intensity" value="0.0"/> + <param name="remove_precursor_peak" value="no"/> + <param name="remove_precursor_tolerance" value="1.5"/> + <param name="clear_mz_range" value="0:0"/> + <param name="max_variable_mods_in_peptide" value="3"/> + <param name="require_variable_mod" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="examples/FRACTIONS/BSA1_F1.mzML"/> + <output name="out" file="CometAdapter_4_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="database" value="examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta"/> + <param name="precursor_mass_tolerance" value="5.0"/> + <param name="precursor_error_units" value="ppm"/> + <param name="isotope_error" value="off"/> + <param name="fragment_mass_tolerance" value="0.01"/> + <param name="fragment_error_units" value="Da"/> + <param name="fragment_bin_offset" value="0.0"/> + <param name="instrument" value="high_res"/> + <param name="enzyme" value="Trypsin"/> + <param name="num_enzyme_termini" value="fully"/> + <param name="missed_cleavages" value="3"/> + <param name="min_peptide_length" value="5"/> + <param name="max_peptide_length" value="63"/> + <param name="num_hits" value="5"/> + <param name="precursor_charge" value="0:0"/> + <param name="override_charge" value="keep known search unknown"/> + <param name="ms_level" value="2"/> + <param name="activation_method" value="ALL"/> + <param name="max_fragment_charge" value="3"/> + <param name="clip_nterm_methionine" value="false"/> + <param name="fixed_modifications" value="Carbamidomethyl (C)"/> + <param name="variable_modifications" value="Met-loss (Protein N-term M)"/> + <param name="binary_modifications" value=""/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_CompNovoCID"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="CompNovoCID_1_input.mzML"/> + <output name="out" file="CompNovoCID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <section name="algorithm"> + <param name="max_number_aa_per_decomp" value="4"/> + <param name="tryptic_only" value="true"/> + <param name="precursor_mass_tolerance" value="0.3"/> + <param name="fragment_mass_tolerance" value="0.3"/> + <param name="max_number_pivot" value="9"/> + <param name="max_subscore_number" value="40"/> + <param name="decomp_weights_precision" value="0.01"/> + <param name="double_charged_iso_threshold" value="0.6"/> + <param name="max_mz" value="2000.0"/> + <param name="min_mz" value="200.0"/> + <param name="max_isotope_to_score" value="3"/> + <param name="max_decomp_weight" value="450.0"/> + <param name="max_isotope" value="3"/> + <param name="missed_cleavages" value="1"/> + <param name="number_of_hits" value="1"/> + <param name="estimate_precursor_mz" value="true"/> + <param name="number_of_prescoring_hits" value="250"/> + <param name="fixed_modifications" value=""/> + <param name="variable_modifications" value=""/> + <param name="residue_set" value="Natural19WithoutI"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_CompNovo"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="CompNovo_1_input.mzML"/> + <output name="out" file="CompNovo_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <section name="algorithm"> + <param name="max_number_aa_per_decomp" value="4"/> + <param name="tryptic_only" value="true"/> + <param name="precursor_mass_tolerance" value="0.3"/> + <param name="fragment_mass_tolerance" value="0.3"/> + <param name="max_number_pivot" value="9"/> + <param name="max_subscore_number" value="40"/> + <param name="decomp_weights_precision" value="0.01"/> + <param name="double_charged_iso_threshold" value="0.6"/> + <param name="max_mz" value="2000.0"/> + <param name="min_mz" value="200.0"/> + <param name="max_isotope_to_score" value="3"/> + <param name="max_decomp_weight" value="450.0"/> + <param name="max_isotope" value="3"/> + <param name="missed_cleavages" value="1"/> + <param name="number_of_hits" value="1"/> + <param name="estimate_precursor_mz" value="true"/> + <param name="number_of_prescoring_hits" value="250"/> + <param name="fixed_modifications" value=""/> + <param name="variable_modifications" value=""/> + <param name="residue_set" value="Natural19WithoutI"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_ConsensusID"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ConsensusID_1_input.idXML"/> + <output name="out" file="ConsensusID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="rt_delta" value="0.1"/> + <param name="mz_delta" value="0.1"/> + <param name="per_spectrum" value="false"/> + <param name="algorithm" value="PEPMatrix"/> + <section name="filter"> + <param name="considered_hits" value="0"/> + <param name="min_support" value="0.0"/> + <param name="count_empty" value="false"/> + <param name="keep_old_scores" value="false"/> + </section> + <section name="PEPIons"> + <param name="mass_tolerance" value="0.5"/> + <param name="min_shared" value="2"/> + </section> + <section name="PEPMatrix"> + <param name="matrix" value="PAM30MS"/> + <param name="penalty" value="5"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ConsensusID_2_input.featureXML"/> + <output name="out" file="ConsensusID_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="rt_delta" value="0.1"/> + <param name="mz_delta" value="0.1"/> + <param name="per_spectrum" value="false"/> + <param name="algorithm" value="average"/> + <section name="filter"> + <param name="considered_hits" value="0"/> + <param name="min_support" value="0.0"/> + <param name="count_empty" value="false"/> + <param name="keep_old_scores" value="false"/> + </section> + <section name="PEPIons"> + <param name="mass_tolerance" value="0.5"/> + <param name="min_shared" value="2"/> + </section> + <section name="PEPMatrix"> + <param name="matrix" value="identity"/> + <param name="penalty" value="5"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ConsensusID_3_input.consensusXML"/> + <output name="out" file="ConsensusID_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="rt_delta" value="0.1"/> + <param name="mz_delta" value="0.1"/> + <param name="per_spectrum" value="false"/> + <param name="algorithm" value="best"/> + <section name="filter"> + <param name="considered_hits" value="0"/> + <param name="min_support" value="0.0"/> + <param name="count_empty" value="false"/> + <param name="keep_old_scores" value="false"/> + </section> + <section name="PEPIons"> + <param name="mass_tolerance" value="0.5"/> + <param name="min_shared" value="2"/> + </section> + <section name="PEPMatrix"> + <param name="matrix" value="identity"/> + <param name="penalty" value="5"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ConsensusID_1_input.idXML"/> + <output name="out" file="ConsensusID_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="rt_delta" value="0.1"/> + <param name="mz_delta" value="0.1"/> + <param name="per_spectrum" value="false"/> + <param name="algorithm" value="PEPMatrix"/> + <section name="filter"> + <param name="considered_hits" value="6"/> + <param name="min_support" value="0.0"/> + <param name="count_empty" value="false"/> + <param name="keep_old_scores" value="false"/> + </section> + <section name="PEPIons"> + <param name="mass_tolerance" value="0.5"/> + <param name="min_shared" value="2"/> + </section> + <section name="PEPMatrix"> + <param name="matrix" value="identity"/> + <param name="penalty" value="5"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ConsensusID_1_input.idXML"/> + <output name="out" file="ConsensusID_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="rt_delta" value="0.1"/> + <param name="mz_delta" value="0.1"/> + <param name="per_spectrum" value="false"/> + <param name="algorithm" value="PEPIons"/> + <section name="filter"> + <param name="considered_hits" value="0"/> + <param name="min_support" value="0.0"/> + <param name="count_empty" value="false"/> + <param name="keep_old_scores" value="false"/> + </section> + <section name="PEPIons"> + <param name="mass_tolerance" value="0.5"/> + <param name="min_shared" value="2"/> + </section> + <section name="PEPMatrix"> + <param name="matrix" value="identity"/> + <param name="penalty" value="5"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ConsensusID_1_input.idXML"/> + <output name="out" file="ConsensusID_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="rt_delta" value="0.1"/> + <param name="mz_delta" value="0.1"/> + <param name="per_spectrum" value="false"/> + <param name="algorithm" value="best"/> + <section name="filter"> + <param name="considered_hits" value="0"/> + <param name="min_support" value="0.5"/> + <param name="count_empty" value="false"/> + <param name="keep_old_scores" value="false"/> + </section> + <section name="PEPIons"> + <param name="mass_tolerance" value="0.5"/> + <param name="min_shared" value="2"/> + </section> + <section name="PEPMatrix"> + <param name="matrix" value="identity"/> + <param name="penalty" value="5"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ConsensusID_6_input.idXML"/> + <output name="out" file="ConsensusID_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="rt_delta" value="0.1"/> + <param name="mz_delta" value="0.1"/> + <param name="per_spectrum" value="true"/> + <param name="algorithm" value="best"/> + <section name="filter"> + <param name="considered_hits" value="0"/> + <param name="min_support" value="0.0"/> + <param name="count_empty" value="false"/> + <param name="keep_old_scores" value="true"/> + </section> + <section name="PEPIons"> + <param name="mass_tolerance" value="0.5"/> + <param name="min_shared" value="2"/> + </section> + <section name="PEPMatrix"> + <param name="matrix" value="identity"/> + <param name="penalty" value="5"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ConsensusID_8_input.idXML"/> + <output name="out" file="ConsensusID_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="rt_delta" value="0.1"/> + <param name="mz_delta" value="0.1"/> + <param name="per_spectrum" value="true"/> + <param name="algorithm" value="best"/> + <section name="filter"> + <param name="considered_hits" value="0"/> + <param name="min_support" value="0.0"/> + <param name="count_empty" value="false"/> + <param name="keep_old_scores" value="true"/> + </section> + <section name="PEPIons"> + <param name="mass_tolerance" value="0.5"/> + <param name="min_shared" value="2"/> + </section> + <section name="PEPMatrix"> + <param name="matrix" value="identity"/> + <param name="penalty" value="5"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_ConsensusMapNormalizer"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="accession_filter" value=""/> + <param name="description_filter" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/> + <output name="out" file="ConsensusMapNormalizer_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="algorithm_type" value="robust_regression"/> + <param name="ratio_threshold" value="0.67"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_CruxAdapter"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="custom_enzyme" value=""/> + <param name="decoy_prefix" value="decoy_"/> + <param name="deisotope" value="false"/> + <param name="report_decoys" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="spectra_comet.mzML"/> + <output name="out" file="CruxAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="database" value="proteins.fasta"/> + <param name="extra_index_args" value=""/> + <param name="extra_search_args" value=""/> + <param name="extra_percolator_args" value=""/> + <param name="precursor_mass_tolerance" value="10.0"/> + <param name="precursor_mass_units" value="ppm"/> + <param name="fragment_bin_offset" value="0.0"/> + <param name="fragment_bin_width" value="0.02"/> + <param name="isotope_error" value=""/> + <param name="run_percolator" value="false"/> + <param name="enzyme" value="trypsin"/> + <param name="digestion" value="full-digest"/> + <param name="allowed_missed_cleavages" value="0"/> + <param name="decoy_format" value="peptide-reverse"/> + <param name="keep_terminal_aminos" value="NC"/> + <param name="cterm_modifications" value=""/> + <param name="nterm_modifications" value=""/> + <param name="modifications" value=""/> + <param name="test_fdr" value="0.01"/> + <param name="train_fdr" value="0.01"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_CVInspector"> +</xml> + <xml name="autotest_DatabaseFilter"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="DatabaseFilter_1.fasta"/> + <param name="id" value="DatabaseFilter_1.idXML"/> + <param name="method" value="whitelist"/> + <output name="out" file="DatabaseFilter_1_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="DatabaseFilter_1.fasta"/> + <param name="id" value="DatabaseFilter_1.idXML"/> + <param name="method" value="blacklist"/> + <output name="out" file="DatabaseFilter_2_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="DatabaseFilter_3.fasta"/> + <param name="id" value="DatabaseFilter_3.mzid"/> + <param name="method" value="whitelist"/> + <output name="out" file="DatabaseFilter_3_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="DatabaseFilter_3.fasta"/> + <param name="id" value="DatabaseFilter_3.mzid"/> + <param name="method" value="blacklist"/> + <output name="out" file="DatabaseFilter_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_DatabaseSuitability"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in_id" value="DatabaseSuitability_in_id.idXML"/> + <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/> + <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/> + <output name="out" file="DatabaseSuitability_out_1.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <section name="algorithm"> + <param name="no_rerank" value="false"/> + <param name="reranking_cutoff_percentile" value="0.01"/> + <param name="FDR" value="0.8"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in_id" value="DatabaseSuitability_in_id.idXML"/> + <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/> + <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/> + <output name="out" file="DatabaseSuitability_out_2.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <section name="algorithm"> + <param name="no_rerank" value="false"/> + <param name="reranking_cutoff_percentile" value="0.9"/> + <param name="FDR" value="1.0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in_id" value="DatabaseSuitability_in_id.idXML"/> + <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/> + <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/> + <output name="out" file="DatabaseSuitability_out_3.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <section name="algorithm"> + <param name="no_rerank" value="true"/> + <param name="reranking_cutoff_percentile" value="0.01"/> + <param name="FDR" value="0.9"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_Decharger"> + <test expect_num_outputs="4"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="Decharger_input.featureXML"/> + <output name="out_cm" file="Decharger_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <output name="out_fm" file="Decharger_output_fm.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="outpairs" file="Decharger_p_output.tmp" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="algorithm"> + <section name="FeatureDeconvolution"> + <param name="charge_min" value="1"/> + <param name="charge_max" value="10"/> + <param name="charge_span_max" value="4"/> + <param name="q_try" value="feature"/> + <param name="retention_max_diff" value="1.0"/> + <param name="retention_max_diff_local" value="1.0"/> + <param name="mass_max_diff" value="0.1"/> + <param name="potential_adducts" value=""H:+:0.7" "Na:+:0.1" "(2)H4H-4:0:0.1:-2:heavy""/> + <param name="max_neutrals" value="0"/> + <param name="max_minority_bound" value="2"/> + <param name="min_rt_overlap" value="0.66"/> + <param name="intensity_filter" value="false"/> + <param name="negative_mode" value="false"/> + <param name="default_map_label" value="decharged features"/> + <param name="verbose_level" value="0"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG,outpairs_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_DecoyDatabase"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="shuffle_max_attempts" value="30"/> + <param name="shuffle_sequence_identity_threshold" value="0.5"/> + <param name="seed" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="DecoyDatabase_1.fasta"/> + <output name="out" file="DecoyDatabase_1_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> + <param name="decoy_string" value="DECOY_"/> + <param name="decoy_string_position" value="prefix"/> + <param name="only_decoy" value="true"/> + <param name="type" value="protein"/> + <param name="method" value="reverse"/> + <param name="enzyme" value="Trypsin"/> + <section name="Decoy"> + <param name="non_shuffle_pattern" value=""/> + <param name="keepPeptideNTerm" value="true"/> + <param name="keepPeptideCTerm" value="true"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="shuffle_max_attempts" value="30"/> + <param name="shuffle_sequence_identity_threshold" value="0.5"/> + <param name="seed" value="42"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="DecoyDatabase_1.fasta"/> + <output name="out" file="DecoyDatabase_2_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> + <param name="decoy_string" value="blabla"/> + <param name="decoy_string_position" value="prefix"/> + <param name="only_decoy" value="false"/> + <param name="type" value="protein"/> + <param name="method" value="shuffle"/> + <param name="enzyme" value="Trypsin"/> + <section name="Decoy"> + <param name="non_shuffle_pattern" value="KRP"/> + <param name="keepPeptideNTerm" value="true"/> + <param name="keepPeptideCTerm" value="true"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="shuffle_max_attempts" value="30"/> + <param name="shuffle_sequence_identity_threshold" value="0.5"/> + <param name="seed" value="42"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="DecoyDatabase_1.fasta"/> + <output name="out" file="DecoyDatabase_3_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> + <param name="decoy_string" value="blabla"/> + <param name="decoy_string_position" value="prefix"/> + <param name="only_decoy" value="false"/> + <param name="type" value="protein"/> + <param name="method" value="shuffle"/> + <param name="enzyme" value="Chymotrypsin"/> + <section name="Decoy"> + <param name="non_shuffle_pattern" value="KR"/> + <param name="keepPeptideNTerm" value="true"/> + <param name="keepPeptideCTerm" value="true"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="shuffle_max_attempts" value="30"/> + <param name="shuffle_sequence_identity_threshold" value="0.5"/> + <param name="seed" value="42"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="DecoyDatabase_4.fasta"/> + <output name="out" file="DecoyDatabase_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> + <param name="decoy_string" value="blabla"/> + <param name="decoy_string_position" value="prefix"/> + <param name="only_decoy" value="false"/> + <param name="type" value="RNA"/> + <param name="method" value="reverse"/> + <param name="enzyme" value="Trypsin"/> + <section name="Decoy"> + <param name="non_shuffle_pattern" value=""/> + <param name="keepPeptideNTerm" value="true"/> + <param name="keepPeptideCTerm" value="true"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_DeMeanderize"> +</xml> + <xml name="autotest_DigestorMotif"> +</xml> + <xml name="autotest_Digestor"> +</xml> + <xml name="autotest_DTAExtractor"> + <test expect_num_outputs="1"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="DTAExtractor_1_input.mzML"/> + <param name="out" value="DTAExtractor"/> + <param name="mz" value=":"/> + <param name="rt" value=":61"/> + <param name="level" value="1,2,3"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="DTAExtractor_1_input.mzML"/> + <param name="out" value="DTAExtractor"/> + <param name="mz" value=":"/> + <param name="rt" value=":"/> + <param name="level" value="1"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="DTAExtractor_1_input.mzML"/> + <param name="out" value="DTAExtractor"/> + <param name="mz" value=":1000"/> + <param name="rt" value=":"/> + <param name="level" value="2"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_EICExtractor"> +</xml> + <xml name="autotest_Epifany"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="conservative_fdr" value="true"/> + <param name="min_psms_extreme_probability" value="0.0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FidoAdapter_1_input.idXML"/> + <output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idxml"/> + <param name="protein_fdr" value="false"/> + <param name="greedy_group_resolution" value="none"/> + <param name="max_psms_extreme_probability" value="1.0"/> + <section name="algorithm"> + <param name="psm_probability_cutoff" value="0.001"/> + <param name="top_PSMs" value="1"/> + <param name="keep_best_PSM_only" value="true"/> + <param name="update_PSM_probabilities" value="true"/> + <param name="user_defined_priors" value="false"/> + <param name="annotate_group_probabilities" value="true"/> + <param name="use_ids_outside_features" value="false"/> + <section name="model_parameters"> + <param name="prot_prior" value="0.7"/> + <param name="pep_emission" value="0.1"/> + <param name="pep_spurious_emission" value="0.001"/> + <param name="pep_prior" value="0.1"/> + <param name="regularize" value="false"/> + <param name="extended_model" value="false"/> + </section> + <section name="loopy_belief_propagation"> + <param name="scheduling_type" value="priority"/> + <param name="convergence_threshold" value="1e-05"/> + <param name="dampening_lambda" value="0.001"/> + <param name="max_nr_iterations" value="2147483647"/> + <param name="p_norm_inference" value="1.0"/> + </section> + <section name="param_optimize"> + <param name="aucweight" value="0.3"/> + <param name="conservative_fdr" value="true"/> + <param name="regularized_fdr" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="conservative_fdr" value="true"/> + <param name="min_psms_extreme_probability" value="0.0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="Epifany_2_input.consensusXML"/> + <output name="out" file="Epifany_2_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="out_type" value="consensusXML"/> + <param name="protein_fdr" value="false"/> + <param name="greedy_group_resolution" value="none"/> + <param name="max_psms_extreme_probability" value="1.0"/> + <section name="algorithm"> + <param name="psm_probability_cutoff" value="0.001"/> + <param name="top_PSMs" value="1"/> + <param name="keep_best_PSM_only" value="true"/> + <param name="update_PSM_probabilities" value="true"/> + <param name="user_defined_priors" value="false"/> + <param name="annotate_group_probabilities" value="true"/> + <param name="use_ids_outside_features" value="false"/> + <section name="model_parameters"> + <param name="prot_prior" value="0.7"/> + <param name="pep_emission" value="0.1"/> + <param name="pep_spurious_emission" value="0.001"/> + <param name="pep_prior" value="0.1"/> + <param name="regularize" value="false"/> + <param name="extended_model" value="false"/> + </section> + <section name="loopy_belief_propagation"> + <param name="scheduling_type" value="priority"/> + <param name="convergence_threshold" value="1e-05"/> + <param name="dampening_lambda" value="0.001"/> + <param name="max_nr_iterations" value="2147483647"/> + <param name="p_norm_inference" value="1.0"/> + </section> + <section name="param_optimize"> + <param name="aucweight" value="0.3"/> + <param name="conservative_fdr" value="true"/> + <param name="regularized_fdr" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="conservative_fdr" value="true"/> + <param name="min_psms_extreme_probability" value="0.0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="Epifany_2_input.consensusXML"/> + <output name="out" file="Epifany_3_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="out_type" value="consensusXML"/> + <param name="protein_fdr" value="false"/> + <param name="greedy_group_resolution" value="none"/> + <param name="max_psms_extreme_probability" value="1.0"/> + <section name="algorithm"> + <param name="psm_probability_cutoff" value="0.001"/> + <param name="top_PSMs" value="1"/> + <param name="keep_best_PSM_only" value="false"/> + <param name="update_PSM_probabilities" value="true"/> + <param name="user_defined_priors" value="false"/> + <param name="annotate_group_probabilities" value="true"/> + <param name="use_ids_outside_features" value="false"/> + <section name="model_parameters"> + <param name="prot_prior" value="0.7"/> + <param name="pep_emission" value="0.1"/> + <param name="pep_spurious_emission" value="0.001"/> + <param name="pep_prior" value="0.1"/> + <param name="regularize" value="false"/> + <param name="extended_model" value="false"/> + </section> + <section name="loopy_belief_propagation"> + <param name="scheduling_type" value="priority"/> + <param name="convergence_threshold" value="1e-05"/> + <param name="dampening_lambda" value="0.001"/> + <param name="max_nr_iterations" value="2147483647"/> + <param name="p_norm_inference" value="1.0"/> + </section> + <section name="param_optimize"> + <param name="aucweight" value="0.3"/> + <param name="conservative_fdr" value="true"/> + <param name="regularized_fdr" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_ERPairFinder"> +</xml> + <xml name="autotest_ExternalCalibration"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ExternalCalibration_1_input.mzML"/> + <output name="out" file="ExternalCalibration_1_MS1_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="offset" value="-5.5"/> + <param name="slope" value="0.0001"/> + <param name="power" value="0.0"/> + <param name="ms_level" value="1"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ExternalCalibration_1_input.mzML"/> + <output name="out" file="ExternalCalibration_2_MS2_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="offset" value="-5.5"/> + <param name="slope" value="0.0001"/> + <param name="power" value="0.0"/> + <param name="ms_level" value="2"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_FalseDiscoveryRate"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/> + <output name="out" file="FalseDiscoveryRate_output_1.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="PSM" value="true"/> + <param name="protein" value="false"/> + <section name="FDR"> + <param name="PSM" value="1.0"/> + <param name="protein" value="1.0"/> + <section name="cleanup"> + <param name="remove_proteins_without_psms" value="true"/> + <param name="remove_psms_without_proteins" value="true"/> + <param name="remove_spectra_without_psms" value="true"/> + </section> + </section> + <section name="algorithm"> + <param name="no_qvalues" value="false"/> + <param name="use_all_hits" value="false"/> + <param name="split_charge_variants" value="false"/> + <param name="treat_runs_separately" value="false"/> + <param name="add_decoy_peptides" value="false"/> + <param name="add_decoy_proteins" value="false"/> + <param name="conservative" value="true"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/> + <output name="out" file="FalseDiscoveryRate_output_2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="PSM" value="true"/> + <param name="protein" value="false"/> + <section name="FDR"> + <param name="PSM" value="1.0"/> + <param name="protein" value="1.0"/> + <section name="cleanup"> + <param name="remove_proteins_without_psms" value="true"/> + <param name="remove_psms_without_proteins" value="true"/> + <param name="remove_spectra_without_psms" value="true"/> + </section> + </section> + <section name="algorithm"> + <param name="no_qvalues" value="false"/> + <param name="use_all_hits" value="false"/> + <param name="split_charge_variants" value="false"/> + <param name="treat_runs_separately" value="true"/> + <param name="add_decoy_peptides" value="false"/> + <param name="add_decoy_proteins" value="false"/> + <param name="conservative" value="true"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/> + <output name="out" file="FalseDiscoveryRate_output_3.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="PSM" value="true"/> + <param name="protein" value="false"/> + <section name="FDR"> + <param name="PSM" value="1.0"/> + <param name="protein" value="1.0"/> + <section name="cleanup"> + <param name="remove_proteins_without_psms" value="true"/> + <param name="remove_psms_without_proteins" value="true"/> + <param name="remove_spectra_without_psms" value="true"/> + </section> + </section> + <section name="algorithm"> + <param name="no_qvalues" value="false"/> + <param name="use_all_hits" value="false"/> + <param name="split_charge_variants" value="true"/> + <param name="treat_runs_separately" value="false"/> + <param name="add_decoy_peptides" value="false"/> + <param name="add_decoy_proteins" value="false"/> + <param name="conservative" value="true"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FalseDiscoveryRate_OMSSA_4.idXML"/> + <output name="out" file="FalseDiscoveryRate_output_4.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="PSM" value="true"/> + <param name="protein" value="false"/> + <section name="FDR"> + <param name="PSM" value="1.0"/> + <param name="protein" value="1.0"/> + <section name="cleanup"> + <param name="remove_proteins_without_psms" value="true"/> + <param name="remove_psms_without_proteins" value="true"/> + <param name="remove_spectra_without_psms" value="true"/> + </section> + </section> + <section name="algorithm"> + <param name="no_qvalues" value="false"/> + <param name="use_all_hits" value="false"/> + <param name="split_charge_variants" value="true"/> + <param name="treat_runs_separately" value="false"/> + <param name="add_decoy_peptides" value="false"/> + <param name="add_decoy_proteins" value="false"/> + <param name="conservative" value="true"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="true"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FalseDiscoveryRate_5_input.idXML"/> + <output name="out" file="FalseDiscoveryRate_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="PSM" value="false"/> + <param name="protein" value="true"/> + <section name="FDR"> + <param name="PSM" value="1.0"/> + <param name="protein" value="1.0"/> + <section name="cleanup"> + <param name="remove_proteins_without_psms" value="true"/> + <param name="remove_psms_without_proteins" value="true"/> + <param name="remove_spectra_without_psms" value="true"/> + </section> + </section> + <section name="algorithm"> + <param name="no_qvalues" value="false"/> + <param name="use_all_hits" value="false"/> + <param name="split_charge_variants" value="false"/> + <param name="treat_runs_separately" value="false"/> + <param name="add_decoy_peptides" value="false"/> + <param name="add_decoy_proteins" value="true"/> + <param name="conservative" value="true"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FalseDiscoveryRate_6_input.idXML"/> + <output name="out" file="FalseDiscoveryRate_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="PSM" value="true"/> + <param name="protein" value="false"/> + <section name="FDR"> + <param name="PSM" value="0.05"/> + <param name="protein" value="1.0"/> + <section name="cleanup"> + <param name="remove_proteins_without_psms" value="true"/> + <param name="remove_psms_without_proteins" value="true"/> + <param name="remove_spectra_without_psms" value="true"/> + </section> + </section> + <section name="algorithm"> + <param name="no_qvalues" value="false"/> + <param name="use_all_hits" value="false"/> + <param name="split_charge_variants" value="false"/> + <param name="treat_runs_separately" value="false"/> + <param name="add_decoy_peptides" value="false"/> + <param name="add_decoy_proteins" value="false"/> + <param name="conservative" value="true"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="true"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FalseDiscoveryRate_7_input.idXML"/> + <output name="out" file="FalseDiscoveryRate_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="PSM" value="false"/> + <param name="protein" value="true"/> + <section name="FDR"> + <param name="PSM" value="1.0"/> + <param name="protein" value="0.3"/> + <section name="cleanup"> + <param name="remove_proteins_without_psms" value="true"/> + <param name="remove_psms_without_proteins" value="true"/> + <param name="remove_spectra_without_psms" value="true"/> + </section> + </section> + <section name="algorithm"> + <param name="no_qvalues" value="false"/> + <param name="use_all_hits" value="false"/> + <param name="split_charge_variants" value="false"/> + <param name="treat_runs_separately" value="false"/> + <param name="add_decoy_peptides" value="false"/> + <param name="add_decoy_proteins" value="false"/> + <param name="conservative" value="true"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_FeatureFinderCentroided"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + <param name="pseudo_rt_shift" value="500.0"/> + </conditional> + <param name="in" value="FeatureFinderCentroided_1_input.mzML"/> + <output name="out" file="FeatureFinderCentroided_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <section name="algorithm"> + <section name="intensity"> + <param name="bins" value="1"/> + </section> + <section name="mass_trace"> + <param name="mz_tolerance" value="0.02"/> + <param name="min_spectra" value="14"/> + <param name="max_missing" value="1"/> + <param name="slope_bound" value="0.1"/> + </section> + <section name="isotopic_pattern"> + <param name="charge_low" value="2"/> + <param name="charge_high" value="2"/> + <param name="mz_tolerance" value="0.02"/> + <param name="intensity_percentage" value="10.0"/> + <param name="intensity_percentage_optional" value="0.1"/> + <param name="optional_fit_improvement" value="2.0"/> + <param name="mass_window_width" value="100.0"/> + <param name="abundance_12C" value="98.93"/> + <param name="abundance_14N" value="99.632"/> + </section> + <section name="seed"> + <param name="min_score" value="0.8"/> + </section> + <section name="fit"> + <param name="max_iterations" value="500"/> + </section> + <section name="feature"> + <param name="min_score" value="0.7"/> + <param name="min_isotope_fit" value="0.8"/> + <param name="min_trace_score" value="0.5"/> + <param name="min_rt_span" value="0.333"/> + <param name="max_rt_span" value="2.5"/> + <param name="rt_shape" value="symmetric"/> + <param name="max_intersection" value="0.35"/> + <param name="reported_mz" value="monoisotopic"/> + </section> + <section name="user-seed"> + <param name="rt_tolerance" value="5.0"/> + <param name="mz_tolerance" value="1.1"/> + <param name="min_score" value="0.5"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_FeatureFinderIdentification"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderIdentification_1_input.mzML"/> + <param name="id" value="FeatureFinderIdentification_1_input.idXML"/> + <output name="out" file="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <section name="extract"> + <param name="batch_size" value="1000"/> + <param name="mz_window" value="0.1"/> + <param name="n_isotopes" value="2"/> + <param name="isotope_pmin" value="0.0"/> + <param name="rt_quantile" value="0.95"/> + <param name="rt_window" value="0.0"/> + </section> + <section name="detect"> + <param name="peak_width" value="60.0"/> + <param name="min_peak_width" value="0.2"/> + <param name="signal_to_noise" value="0.8"/> + <param name="mapping_tolerance" value="0.0"/> + </section> + <section name="svm"> + <param name="samples" value="0"/> + <param name="no_selection" value="false"/> + <param name="kernel" value="RBF"/> + <param name="xval" value="5"/> + <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/> + <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/> + <param name="epsilon" value="0.001"/> + <param name="cache_size" value="100.0"/> + <param name="no_shrinking" value="false"/> + <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/> + <param name="min_prob" value="0.0"/> + </section> + <section name="model"> + <param name="type" value="none"/> + <param name="add_zeros" value="0.2"/> + <param name="unweighted_fit" value="false"/> + <param name="no_imputation" value="false"/> + <param name="each_trace" value="false"/> + <section name="check"> + <param name="min_area" value="1.0"/> + <param name="boundaries" value="0.5"/> + <param name="width" value="10.0"/> + <param name="asymmetry" value="10.0"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderIdentification_1_input.mzML"/> + <param name="id" value="FeatureFinderIdentification_1_input.idXML"/> + <output name="out" file="FeatureFinderIdentification_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <section name="extract"> + <param name="batch_size" value="1000"/> + <param name="mz_window" value="0.1"/> + <param name="n_isotopes" value="2"/> + <param name="isotope_pmin" value="0.0"/> + <param name="rt_quantile" value="0.95"/> + <param name="rt_window" value="0.0"/> + </section> + <section name="detect"> + <param name="peak_width" value="60.0"/> + <param name="min_peak_width" value="0.2"/> + <param name="signal_to_noise" value="0.8"/> + <param name="mapping_tolerance" value="0.0"/> + </section> + <section name="svm"> + <param name="samples" value="0"/> + <param name="no_selection" value="false"/> + <param name="kernel" value="RBF"/> + <param name="xval" value="5"/> + <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/> + <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/> + <param name="epsilon" value="0.001"/> + <param name="cache_size" value="100.0"/> + <param name="no_shrinking" value="false"/> + <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/> + <param name="min_prob" value="0.0"/> + </section> + <section name="model"> + <param name="type" value="symmetric"/> + <param name="add_zeros" value="0.2"/> + <param name="unweighted_fit" value="false"/> + <param name="no_imputation" value="false"/> + <param name="each_trace" value="false"/> + <section name="check"> + <param name="min_area" value="1.0"/> + <param name="boundaries" value="0.5"/> + <param name="width" value="10.0"/> + <param name="asymmetry" value="10.0"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_FeatureFinderIsotopeWavelet"> +</xml> + <xml name="autotest_FeatureFinderMetaboIdent"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderMetaboIdent_1_input.mzML"/> + <param name="id" value="FeatureFinderMetaboIdent_1_input.tsv" ftype="tabular"/> + <output name="out" file="FeatureFinderMetaboIdent_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <section name="extract"> + <param name="mz_window" value="5.0"/> + <param name="n_isotopes" value="2"/> + <param name="isotope_pmin" value="0.0"/> + <param name="rt_window" value="20.0"/> + </section> + <section name="detect"> + <param name="peak_width" value="3.0"/> + <param name="min_peak_width" value="0.2"/> + <param name="signal_to_noise" value="0.8"/> + </section> + <section name="model"> + <param name="type" value="symmetric"/> + <param name="add_zeros" value="0.2"/> + <param name="unweighted_fit" value="false"/> + <param name="no_imputation" value="false"/> + <param name="each_trace" value="false"/> + <section name="check"> + <param name="min_area" value="1.0"/> + <param name="boundaries" value="0.5"/> + <param name="width" value="10.0"/> + <param name="asymmetry" value="10.0"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_FeatureFinderMetabo"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderMetabo_1_input.mzML"/> + <output name="out" file="FeatureFinderMetabo_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <section name="algorithm"> + <section name="common"> + <param name="noise_threshold_int" value="10.0"/> + <param name="chrom_peak_snr" value="3.0"/> + <param name="chrom_fwhm" value="5.0"/> + </section> + <section name="mtd"> + <param name="mass_error_ppm" value="20.0"/> + <param name="reestimate_mt_sd" value="true"/> + <param name="quant_method" value="area"/> + <param name="trace_termination_criterion" value="outlier"/> + <param name="trace_termination_outliers" value="5"/> + <param name="min_sample_rate" value="0.5"/> + <param name="min_trace_length" value="5.0"/> + <param name="max_trace_length" value="300.0"/> + </section> + <section name="epd"> + <param name="enabled" value="true"/> + <param name="width_filtering" value="off"/> + <param name="min_fwhm" value="3.0"/> + <param name="max_fwhm" value="60.0"/> + <param name="masstrace_snr_filtering" value="false"/> + </section> + <section name="ffm"> + <param name="local_rt_range" value="10.0"/> + <param name="local_mz_range" value="6.5"/> + <param name="charge_lower_bound" value="1"/> + <param name="charge_upper_bound" value="3"/> + <param name="report_summed_ints" value="false"/> + <param name="enable_RT_filtering" value="true"/> + <param name="isotope_filtering_model" value="metabolites (5% RMS)"/> + <param name="mz_scoring_13C" value="true"/> + <param name="use_smoothed_intensities" value="true"/> + <param name="report_convex_hulls" value="false"/> + <param name="remove_single_traces" value="false"/> + <param name="mz_scoring_by_elements" value="false"/> + <param name="elements" value="CHNOPS"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderMetabo_2_input.mzML"/> + <output name="out" file="FeatureFinderMetabo_2_noEPD_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <section name="algorithm"> + <section name="common"> + <param name="noise_threshold_int" value="100.0"/> + <param name="chrom_peak_snr" value="0.0"/> + <param name="chrom_fwhm" value="100.0"/> + </section> + <section name="mtd"> + <param name="mass_error_ppm" value="5.0"/> + <param name="reestimate_mt_sd" value="true"/> + <param name="quant_method" value="median"/> + <param name="trace_termination_criterion" value="sample_rate"/> + <param name="trace_termination_outliers" value="2"/> + <param name="min_sample_rate" value="0.01"/> + <param name="min_trace_length" value="30.0"/> + <param name="max_trace_length" value="3000.0"/> + </section> + <section name="epd"> + <param name="enabled" value="false"/> + <param name="width_filtering" value="off"/> + <param name="min_fwhm" value="10.0"/> + <param name="max_fwhm" value="80.0"/> + <param name="masstrace_snr_filtering" value="false"/> + </section> + <section name="ffm"> + <param name="local_rt_range" value="10.0"/> + <param name="local_mz_range" value="4.5"/> + <param name="charge_lower_bound" value="1"/> + <param name="charge_upper_bound" value="3"/> + <param name="report_summed_ints" value="false"/> + <param name="enable_RT_filtering" value="false"/> + <param name="isotope_filtering_model" value="none"/> + <param name="mz_scoring_13C" value="false"/> + <param name="use_smoothed_intensities" value="false"/> + <param name="report_convex_hulls" value="true"/> + <param name="remove_single_traces" value="false"/> + <param name="mz_scoring_by_elements" value="false"/> + <param name="elements" value="CHNOPS"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderMetabo_3_input.mzML"/> + <output name="out" file="FeatureFinderMetabo_3.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_chrom" file="FeatureFinderMetabo_3_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <section name="common"> + <param name="noise_threshold_int" value="10.0"/> + <param name="chrom_peak_snr" value="3.0"/> + <param name="chrom_fwhm" value="5.0"/> + </section> + <section name="mtd"> + <param name="mass_error_ppm" value="5.0"/> + <param name="reestimate_mt_sd" value="true"/> + <param name="quant_method" value="area"/> + <param name="trace_termination_criterion" value="outlier"/> + <param name="trace_termination_outliers" value="5"/> + <param name="min_sample_rate" value="0.5"/> + <param name="min_trace_length" value="5.0"/> + <param name="max_trace_length" value="-1.0"/> + </section> + <section name="epd"> + <param name="enabled" value="true"/> + <param name="width_filtering" value="fixed"/> + <param name="min_fwhm" value="3.0"/> + <param name="max_fwhm" value="60.0"/> + <param name="masstrace_snr_filtering" value="false"/> + </section> + <section name="ffm"> + <param name="local_rt_range" value="10.0"/> + <param name="local_mz_range" value="6.5"/> + <param name="charge_lower_bound" value="1"/> + <param name="charge_upper_bound" value="3"/> + <param name="report_summed_ints" value="false"/> + <param name="enable_RT_filtering" value="true"/> + <param name="isotope_filtering_model" value="none"/> + <param name="mz_scoring_13C" value="true"/> + <param name="use_smoothed_intensities" value="true"/> + <param name="report_convex_hulls" value="true"/> + <param name="remove_single_traces" value="false"/> + <param name="mz_scoring_by_elements" value="false"/> + <param name="elements" value="CHNOPS"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderMetabo_3_input.mzML"/> + <output name="out" file="FeatureFinderMetabo_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_chrom" file="FeatureFinderMetabo_4_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <section name="common"> + <param name="noise_threshold_int" value="10.0"/> + <param name="chrom_peak_snr" value="3.0"/> + <param name="chrom_fwhm" value="5.0"/> + </section> + <section name="mtd"> + <param name="mass_error_ppm" value="5.0"/> + <param name="reestimate_mt_sd" value="true"/> + <param name="quant_method" value="area"/> + <param name="trace_termination_criterion" value="outlier"/> + <param name="trace_termination_outliers" value="5"/> + <param name="min_sample_rate" value="0.5"/> + <param name="min_trace_length" value="5.0"/> + <param name="max_trace_length" value="-1.0"/> + </section> + <section name="epd"> + <param name="enabled" value="true"/> + <param name="width_filtering" value="fixed"/> + <param name="min_fwhm" value="3.0"/> + <param name="max_fwhm" value="60.0"/> + <param name="masstrace_snr_filtering" value="false"/> + </section> + <section name="ffm"> + <param name="local_rt_range" value="10.0"/> + <param name="local_mz_range" value="6.5"/> + <param name="charge_lower_bound" value="1"/> + <param name="charge_upper_bound" value="3"/> + <param name="report_summed_ints" value="false"/> + <param name="enable_RT_filtering" value="true"/> + <param name="isotope_filtering_model" value="none"/> + <param name="mz_scoring_13C" value="true"/> + <param name="use_smoothed_intensities" value="true"/> + <param name="report_convex_hulls" value="true"/> + <param name="remove_single_traces" value="true"/> + <param name="mz_scoring_by_elements" value="false"/> + <param name="elements" value="CHNOPS"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderMetabo_1_input.mzML"/> + <output name="out" file="FeatureFinderMetabo_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <section name="algorithm"> + <section name="common"> + <param name="noise_threshold_int" value="10.0"/> + <param name="chrom_peak_snr" value="3.0"/> + <param name="chrom_fwhm" value="5.0"/> + </section> + <section name="mtd"> + <param name="mass_error_ppm" value="20.0"/> + <param name="reestimate_mt_sd" value="true"/> + <param name="quant_method" value="max_height"/> + <param name="trace_termination_criterion" value="outlier"/> + <param name="trace_termination_outliers" value="5"/> + <param name="min_sample_rate" value="0.5"/> + <param name="min_trace_length" value="5.0"/> + <param name="max_trace_length" value="300.0"/> + </section> + <section name="epd"> + <param name="enabled" value="true"/> + <param name="width_filtering" value="off"/> + <param name="min_fwhm" value="3.0"/> + <param name="max_fwhm" value="60.0"/> + <param name="masstrace_snr_filtering" value="false"/> + </section> + <section name="ffm"> + <param name="local_rt_range" value="10.0"/> + <param name="local_mz_range" value="6.5"/> + <param name="charge_lower_bound" value="1"/> + <param name="charge_upper_bound" value="3"/> + <param name="report_summed_ints" value="false"/> + <param name="enable_RT_filtering" value="true"/> + <param name="isotope_filtering_model" value="metabolites (5% RMS)"/> + <param name="mz_scoring_13C" value="true"/> + <param name="use_smoothed_intensities" value="true"/> + <param name="report_convex_hulls" value="false"/> + <param name="remove_single_traces" value="false"/> + <param name="mz_scoring_by_elements" value="false"/> + <param name="elements" value="CHNOPS"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_FeatureFinderMRM"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderMRM_1_input.mzML"/> + <output name="out" file="FeatureFinderMRM_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <section name="algorithm"> + <param name="min_rt_distance" value="10.0"/> + <param name="min_num_peaks_per_feature" value="5"/> + <param name="min_signal_to_noise_ratio" value="2.0"/> + <param name="write_debug_files" value="false"/> + <param name="resample_traces" value="false"/> + <param name="write_debuginfo" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_FeatureFinderMultiplex"> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderMultiplex_1_input.mzML"/> + <output name="out" file="FeatureFinderMultiplex_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_multiplets" file="FeatureFinderMultiplex_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="algorithm"> + <param name="labels" value="[Dimethyl0][Dimethyl8]"/> + <param name="charge" value="1:4"/> + <param name="isotopes_per_peptide" value="3:6"/> + <param name="rt_typical" value="90.0"/> + <param name="rt_band" value="10.0"/> + <param name="rt_min" value="5.0"/> + <param name="mz_tolerance" value="40.0"/> + <param name="mz_unit" value="ppm"/> + <param name="intensity_cutoff" value="10.0"/> + <param name="peptide_similarity" value="0.8"/> + <param name="averagine_similarity" value="0.75"/> + <param name="averagine_similarity_scaling" value="0.75"/> + <param name="missed_cleavages" value="1"/> + <param name="spectrum_type" value="automatic"/> + <param name="averagine_type" value="peptide"/> + <param name="knock_out" value="false"/> + </section> + <section name="labels"> + <param name="Arg6" value="6.0201290268"/> + <param name="Arg10" value="10.0082686"/> + <param name="Lys4" value="4.0251069836"/> + <param name="Lys6" value="6.0201290268"/> + <param name="Lys8" value="8.0141988132"/> + <param name="Leu3" value="3.01883"/> + <param name="Dimethyl0" value="28.0313"/> + <param name="Dimethyl4" value="32.056407"/> + <param name="Dimethyl6" value="34.063117"/> + <param name="Dimethyl8" value="36.07567"/> + <param name="ICPL0" value="105.021464"/> + <param name="ICPL4" value="109.046571"/> + <param name="ICPL6" value="111.041593"/> + <param name="ICPL10" value="115.0667"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderMultiplex_2_input.mzML"/> + <output name="out" file="FeatureFinderMultiplex_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_multiplets" file="FeatureFinderMultiplex_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="algorithm"> + <param name="labels" value="[][Lys8,Arg10]"/> + <param name="charge" value="1:4"/> + <param name="isotopes_per_peptide" value="3:6"/> + <param name="rt_typical" value="40.0"/> + <param name="rt_band" value="5.0"/> + <param name="rt_min" value="2.0"/> + <param name="mz_tolerance" value="6.0"/> + <param name="mz_unit" value="ppm"/> + <param name="intensity_cutoff" value="1000.0"/> + <param name="peptide_similarity" value="0.5"/> + <param name="averagine_similarity" value="0.4"/> + <param name="averagine_similarity_scaling" value="0.75"/> + <param name="missed_cleavages" value="0"/> + <param name="spectrum_type" value="automatic"/> + <param name="averagine_type" value="peptide"/> + <param name="knock_out" value="false"/> + </section> + <section name="labels"> + <param name="Arg6" value="6.0201290268"/> + <param name="Arg10" value="10.0082686"/> + <param name="Lys4" value="4.0251069836"/> + <param name="Lys6" value="6.0201290268"/> + <param name="Lys8" value="8.0141988132"/> + <param name="Leu3" value="3.01883"/> + <param name="Dimethyl0" value="28.0313"/> + <param name="Dimethyl4" value="32.056407"/> + <param name="Dimethyl6" value="34.063117"/> + <param name="Dimethyl8" value="36.07567"/> + <param name="ICPL0" value="105.021464"/> + <param name="ICPL4" value="109.046571"/> + <param name="ICPL6" value="111.041593"/> + <param name="ICPL10" value="115.0667"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderMultiplex_3_input.mzML"/> + <output name="out" file="FeatureFinderMultiplex_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_multiplets" file="FeatureFinderMultiplex_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="algorithm"> + <param name="labels" value="[]"/> + <param name="charge" value="5:15"/> + <param name="isotopes_per_peptide" value="5:10"/> + <param name="rt_typical" value="45.0"/> + <param name="rt_band" value="5.0"/> + <param name="rt_min" value="2.0"/> + <param name="mz_tolerance" value="6.0"/> + <param name="mz_unit" value="ppm"/> + <param name="intensity_cutoff" value="200.0"/> + <param name="peptide_similarity" value="0.5"/> + <param name="averagine_similarity" value="0.4"/> + <param name="averagine_similarity_scaling" value="0.75"/> + <param name="missed_cleavages" value="0"/> + <param name="spectrum_type" value="automatic"/> + <param name="averagine_type" value="RNA"/> + <param name="knock_out" value="false"/> + </section> + <section name="labels"> + <param name="Arg6" value="6.0201290268"/> + <param name="Arg10" value="10.0082686"/> + <param name="Lys4" value="4.0251069836"/> + <param name="Lys6" value="6.0201290268"/> + <param name="Lys8" value="8.0141988132"/> + <param name="Leu3" value="3.01883"/> + <param name="Dimethyl0" value="28.0313"/> + <param name="Dimethyl4" value="32.056407"/> + <param name="Dimethyl6" value="34.063117"/> + <param name="Dimethyl8" value="36.07567"/> + <param name="ICPL0" value="105.021464"/> + <param name="ICPL4" value="109.046571"/> + <param name="ICPL6" value="111.041593"/> + <param name="ICPL10" value="115.0667"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderMultiplex_4_input.mzML"/> + <output name="out" file="FeatureFinderMultiplex_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_multiplets" file="FeatureFinderMultiplex_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="algorithm"> + <param name="labels" value="[]"/> + <param name="charge" value="5:15"/> + <param name="isotopes_per_peptide" value="5:10"/> + <param name="rt_typical" value="45.0"/> + <param name="rt_band" value="5.0"/> + <param name="rt_min" value="2.0"/> + <param name="mz_tolerance" value="6.0"/> + <param name="mz_unit" value="ppm"/> + <param name="intensity_cutoff" value="200.0"/> + <param name="peptide_similarity" value="0.5"/> + <param name="averagine_similarity" value="0.4"/> + <param name="averagine_similarity_scaling" value="0.75"/> + <param name="missed_cleavages" value="0"/> + <param name="spectrum_type" value="automatic"/> + <param name="averagine_type" value="DNA"/> + <param name="knock_out" value="false"/> + </section> + <section name="labels"> + <param name="Arg6" value="6.0201290268"/> + <param name="Arg10" value="10.0082686"/> + <param name="Lys4" value="4.0251069836"/> + <param name="Lys6" value="6.0201290268"/> + <param name="Lys8" value="8.0141988132"/> + <param name="Leu3" value="3.01883"/> + <param name="Dimethyl0" value="28.0313"/> + <param name="Dimethyl4" value="32.056407"/> + <param name="Dimethyl6" value="34.063117"/> + <param name="Dimethyl8" value="36.07567"/> + <param name="ICPL0" value="105.021464"/> + <param name="ICPL4" value="109.046571"/> + <param name="ICPL6" value="111.041593"/> + <param name="ICPL10" value="115.0667"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderMultiplex_5_input.mzML"/> + <output name="out" file="FeatureFinderMultiplex_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_multiplets" file="FeatureFinderMultiplex_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="algorithm"> + <param name="labels" value="[Dimethyl0][Dimethyl6]"/> + <param name="charge" value="1:5"/> + <param name="isotopes_per_peptide" value="3:6"/> + <param name="rt_typical" value="50.0"/> + <param name="rt_band" value="3.0"/> + <param name="rt_min" value="8.0"/> + <param name="mz_tolerance" value="10.0"/> + <param name="mz_unit" value="ppm"/> + <param name="intensity_cutoff" value="10000000.0"/> + <param name="peptide_similarity" value="0.95"/> + <param name="averagine_similarity" value="0.8"/> + <param name="averagine_similarity_scaling" value="0.95"/> + <param name="missed_cleavages" value="3"/> + <param name="spectrum_type" value="profile"/> + <param name="averagine_type" value="peptide"/> + <param name="knock_out" value="false"/> + </section> + <section name="labels"> + <param name="Arg6" value="6.0201290268"/> + <param name="Arg10" value="10.0082686"/> + <param name="Lys4" value="4.0251069836"/> + <param name="Lys6" value="6.0201290268"/> + <param name="Lys8" value="8.0141988132"/> + <param name="Leu3" value="3.01883"/> + <param name="Dimethyl0" value="28.0313"/> + <param name="Dimethyl4" value="32.056407"/> + <param name="Dimethyl6" value="34.063117"/> + <param name="Dimethyl8" value="36.07567"/> + <param name="ICPL0" value="105.021464"/> + <param name="ICPL4" value="109.046571"/> + <param name="ICPL6" value="111.041593"/> + <param name="ICPL10" value="115.0667"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderMultiplex_6_input.mzML"/> + <output name="out" file="FeatureFinderMultiplex_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_multiplets" file="FeatureFinderMultiplex_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="algorithm"> + <param name="labels" value="[Dimethyl0][Dimethyl6]"/> + <param name="charge" value="1:5"/> + <param name="isotopes_per_peptide" value="3:6"/> + <param name="rt_typical" value="50.0"/> + <param name="rt_band" value="3.0"/> + <param name="rt_min" value="8.0"/> + <param name="mz_tolerance" value="10.0"/> + <param name="mz_unit" value="ppm"/> + <param name="intensity_cutoff" value="10000000.0"/> + <param name="peptide_similarity" value="0.95"/> + <param name="averagine_similarity" value="0.8"/> + <param name="averagine_similarity_scaling" value="1.0"/> + <param name="missed_cleavages" value="3"/> + <param name="spectrum_type" value="profile"/> + <param name="averagine_type" value="peptide"/> + <param name="knock_out" value="false"/> + </section> + <section name="labels"> + <param name="Arg6" value="6.0201290268"/> + <param name="Arg10" value="10.0082686"/> + <param name="Lys4" value="4.0251069836"/> + <param name="Lys6" value="6.0201290268"/> + <param name="Lys8" value="8.0141988132"/> + <param name="Leu3" value="3.01883"/> + <param name="Dimethyl0" value="28.0313"/> + <param name="Dimethyl4" value="32.056407"/> + <param name="Dimethyl6" value="34.063117"/> + <param name="Dimethyl8" value="36.07567"/> + <param name="ICPL0" value="105.021464"/> + <param name="ICPL4" value="109.046571"/> + <param name="ICPL6" value="111.041593"/> + <param name="ICPL10" value="115.0667"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderMultiplex_7_input.mzML"/> + <output name="out" file="FeatureFinderMultiplex_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_multiplets" file="FeatureFinderMultiplex_7_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="algorithm"> + <param name="labels" value="[][Dimethyl4]"/> + <param name="charge" value="1:4"/> + <param name="isotopes_per_peptide" value="3:6"/> + <param name="rt_typical" value="40.0"/> + <param name="rt_band" value="5.0"/> + <param name="rt_min" value="2.0"/> + <param name="mz_tolerance" value="6.0"/> + <param name="mz_unit" value="ppm"/> + <param name="intensity_cutoff" value="1000.0"/> + <param name="peptide_similarity" value="0.5"/> + <param name="averagine_similarity" value="0.4"/> + <param name="averagine_similarity_scaling" value="0.75"/> + <param name="missed_cleavages" value="0"/> + <param name="spectrum_type" value="automatic"/> + <param name="averagine_type" value="peptide"/> + <param name="knock_out" value="false"/> + </section> + <section name="labels"> + <param name="Arg6" value="6.0201290268"/> + <param name="Arg10" value="10.0082686"/> + <param name="Lys4" value="4.0251069836"/> + <param name="Lys6" value="6.0201290268"/> + <param name="Lys8" value="8.0141988132"/> + <param name="Leu3" value="3.01883"/> + <param name="Dimethyl0" value="28.0313"/> + <param name="Dimethyl4" value="31.0094"/> + <param name="Dimethyl6" value="34.063117"/> + <param name="Dimethyl8" value="36.07567"/> + <param name="ICPL0" value="105.021464"/> + <param name="ICPL4" value="109.046571"/> + <param name="ICPL6" value="111.041593"/> + <param name="ICPL10" value="115.0667"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderMultiplex_8_input.mzML"/> + <output name="out" file="FeatureFinderMultiplex_8_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_multiplets" file="FeatureFinderMultiplex_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="algorithm"> + <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/> + <param name="charge" value="1:7"/> + <param name="isotopes_per_peptide" value="3:8"/> + <param name="rt_typical" value="50.0"/> + <param name="rt_band" value="3.0"/> + <param name="rt_min" value="8.0"/> + <param name="mz_tolerance" value="10.0"/> + <param name="mz_unit" value="ppm"/> + <param name="intensity_cutoff" value="10.0"/> + <param name="peptide_similarity" value="0.2"/> + <param name="averagine_similarity" value="0.25"/> + <param name="averagine_similarity_scaling" value="0.95"/> + <param name="missed_cleavages" value="4"/> + <param name="spectrum_type" value="automatic"/> + <param name="averagine_type" value="peptide"/> + <param name="knock_out" value="true"/> + </section> + <section name="labels"> + <param name="Arg6" value="6.0201290268"/> + <param name="Arg10" value="10.0082686"/> + <param name="Lys4" value="4.0251069836"/> + <param name="Lys6" value="6.0201290268"/> + <param name="Lys8" value="8.0141988132"/> + <param name="Leu3" value="3.01883"/> + <param name="Dimethyl0" value="28.0313"/> + <param name="Dimethyl4" value="32.056407"/> + <param name="Dimethyl6" value="34.063117"/> + <param name="Dimethyl8" value="36.07567"/> + <param name="ICPL0" value="105.021464"/> + <param name="ICPL4" value="109.046571"/> + <param name="ICPL6" value="111.041593"/> + <param name="ICPL10" value="115.0667"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderMultiplex_9_input.mzML"/> + <output name="out" file="FeatureFinderMultiplex_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_multiplets" file="FeatureFinderMultiplex_9_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="algorithm"> + <param name="labels" value="[0][6.03705]"/> + <param name="charge" value="2:8"/> + <param name="isotopes_per_peptide" value="3:8"/> + <param name="rt_typical" value="40.0"/> + <param name="rt_band" value="0.0"/> + <param name="rt_min" value="4.0"/> + <param name="mz_tolerance" value="10.0"/> + <param name="mz_unit" value="ppm"/> + <param name="intensity_cutoff" value="1000.0"/> + <param name="peptide_similarity" value="0.5"/> + <param name="averagine_similarity" value="0.4"/> + <param name="averagine_similarity_scaling" value="0.95"/> + <param name="missed_cleavages" value="0"/> + <param name="spectrum_type" value="centroid"/> + <param name="averagine_type" value="peptide"/> + <param name="knock_out" value="false"/> + </section> + <section name="labels"> + <param name="Arg6" value="6.0201290268"/> + <param name="Arg10" value="10.0082686"/> + <param name="Lys4" value="4.0251069836"/> + <param name="Lys6" value="6.0201290268"/> + <param name="Lys8" value="8.0141988132"/> + <param name="Leu3" value="3.01883"/> + <param name="Dimethyl0" value="28.0313"/> + <param name="Dimethyl4" value="32.056407"/> + <param name="Dimethyl6" value="34.063117"/> + <param name="Dimethyl8" value="36.07567"/> + <param name="ICPL0" value="105.021464"/> + <param name="ICPL4" value="109.046571"/> + <param name="ICPL6" value="111.041593"/> + <param name="ICPL10" value="115.0667"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderMultiplex_10_input.mzML"/> + <output name="out" file="FeatureFinderMultiplex_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_multiplets" file="FeatureFinderMultiplex_10_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="algorithm"> + <param name="labels" value="[Dimethyl0][Dimethyl6]"/> + <param name="charge" value="1:7"/> + <param name="isotopes_per_peptide" value="3:6"/> + <param name="rt_typical" value="50.0"/> + <param name="rt_band" value="5.0"/> + <param name="rt_min" value="8.0"/> + <param name="mz_tolerance" value="6.0"/> + <param name="mz_unit" value="ppm"/> + <param name="intensity_cutoff" value="10.0"/> + <param name="peptide_similarity" value="0.4"/> + <param name="averagine_similarity" value="0.5"/> + <param name="averagine_similarity_scaling" value="0.95"/> + <param name="missed_cleavages" value="3"/> + <param name="spectrum_type" value="profile"/> + <param name="averagine_type" value="peptide"/> + <param name="knock_out" value="true"/> + </section> + <section name="labels"> + <param name="Arg6" value="6.0201290268"/> + <param name="Arg10" value="10.0082686"/> + <param name="Lys4" value="4.0251069836"/> + <param name="Lys6" value="6.0201290268"/> + <param name="Lys8" value="8.0141988132"/> + <param name="Leu3" value="3.01883"/> + <param name="Dimethyl0" value="28.0313"/> + <param name="Dimethyl4" value="32.056407"/> + <param name="Dimethyl6" value="34.063117"/> + <param name="Dimethyl8" value="36.07567"/> + <param name="ICPL0" value="105.021464"/> + <param name="ICPL4" value="109.046571"/> + <param name="ICPL6" value="111.041593"/> + <param name="ICPL10" value="115.0667"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderMultiplex_11_input.mzML"/> + <output name="out" file="FeatureFinderMultiplex_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <section name="algorithm"> + <param name="labels" value="[]"/> + <param name="charge" value="1:4"/> + <param name="isotopes_per_peptide" value="3:6"/> + <param name="rt_typical" value="1e-05"/> + <param name="rt_band" value="0.0"/> + <param name="rt_min" value="0.0"/> + <param name="mz_tolerance" value="10.0"/> + <param name="mz_unit" value="ppm"/> + <param name="intensity_cutoff" value="1000.0"/> + <param name="peptide_similarity" value="0.5"/> + <param name="averagine_similarity" value="0.7"/> + <param name="averagine_similarity_scaling" value="0.95"/> + <param name="missed_cleavages" value="0"/> + <param name="spectrum_type" value="automatic"/> + <param name="averagine_type" value="peptide"/> + <param name="knock_out" value="false"/> + </section> + <section name="labels"> + <param name="Arg6" value="6.0201290268"/> + <param name="Arg10" value="10.0082686"/> + <param name="Lys4" value="4.0251069836"/> + <param name="Lys6" value="6.0201290268"/> + <param name="Lys8" value="8.0141988132"/> + <param name="Leu3" value="3.01883"/> + <param name="Dimethyl0" value="28.0313"/> + <param name="Dimethyl4" value="32.056407"/> + <param name="Dimethyl6" value="34.063117"/> + <param name="Dimethyl8" value="36.07567"/> + <param name="ICPL0" value="105.021464"/> + <param name="ICPL4" value="109.046571"/> + <param name="ICPL6" value="111.041593"/> + <param name="ICPL10" value="115.0667"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_FeatureFinderSuperHirn"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderSuperHirn_input_1.mzML"/> + <output name="out" file="FeatureFinderSuperHirn_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <section name="algorithm"> + <section name="centroiding"> + <param name="active" value="false"/> + <param name="window_width" value="5"/> + <param name="absolute_isotope_mass_precision" value="0.01"/> + <param name="relative_isotope_mass_precision" value="10.0"/> + <param name="minimal_peak_height" value="0.0"/> + <param name="min_ms_signal_intensity" value="50.0"/> + </section> + <section name="ms1"> + <param name="precursor_detection_scan_levels" value="1"/> + <param name="max_inter_scan_distance" value="0"/> + <param name="tr_resolution" value="0.01"/> + <param name="intensity_threshold" value="1000.0"/> + <param name="max_inter_scan_rt_distance" value="0.1"/> + <param name="min_nb_cluster_members" value="4"/> + <param name="detectable_isotope_factor" value="0.05"/> + <param name="intensity_cv" value="0.9"/> + <param name="retention_time_tolerance" value="0.5"/> + <param name="mz_tolerance" value="0.0"/> + </section> + <section name="ms1_feature_merger"> + <param name="active" value="true"/> + <param name="tr_resolution" value="0.01"/> + <param name="initial_apex_tr_tolerance" value="5.0"/> + <param name="feature_merging_tr_tolerance" value="1.0"/> + <param name="intensity_variation_percentage" value="25.0"/> + <param name="ppm_tolerance_for_mz_clustering" value="10.0"/> + </section> + <section name="ms1_feature_selection_options"> + <param name="start_elution_window" value="0.0"/> + <param name="end_elution_window" value="180.0"/> + <param name="mz_range_min" value="0.0"/> + <param name="mz_range_max" value="2000.0"/> + <param name="chrg_range_min" value="1"/> + <param name="chrg_range_max" value="5"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureFinderSuperHirn_input_2.mzML"/> + <output name="out" file="FeatureFinderSuperHirn_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <section name="algorithm"> + <section name="centroiding"> + <param name="active" value="true"/> + <param name="window_width" value="5"/> + <param name="absolute_isotope_mass_precision" value="0.01"/> + <param name="relative_isotope_mass_precision" value="10.0"/> + <param name="minimal_peak_height" value="0.0"/> + <param name="min_ms_signal_intensity" value="50.0"/> + </section> + <section name="ms1"> + <param name="precursor_detection_scan_levels" value="1"/> + <param name="max_inter_scan_distance" value="0"/> + <param name="tr_resolution" value="0.01"/> + <param name="intensity_threshold" value="1000.0"/> + <param name="max_inter_scan_rt_distance" value="0.1"/> + <param name="min_nb_cluster_members" value="4"/> + <param name="detectable_isotope_factor" value="0.05"/> + <param name="intensity_cv" value="0.9"/> + <param name="retention_time_tolerance" value="0.5"/> + <param name="mz_tolerance" value="0.0"/> + </section> + <section name="ms1_feature_merger"> + <param name="active" value="true"/> + <param name="tr_resolution" value="0.01"/> + <param name="initial_apex_tr_tolerance" value="5.0"/> + <param name="feature_merging_tr_tolerance" value="1.0"/> + <param name="intensity_variation_percentage" value="25.0"/> + <param name="ppm_tolerance_for_mz_clustering" value="10.0"/> + </section> + <section name="ms1_feature_selection_options"> + <param name="start_elution_window" value="0.0"/> + <param name="end_elution_window" value="180.0"/> + <param name="mz_range_min" value="0.0"/> + <param name="mz_range_max" value="2000.0"/> + <param name="chrg_range_min" value="1"/> + <param name="chrg_range_max" value="5"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_FeatureLinkerLabeled"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/> + <output name="out" file="FeatureLinkerLabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="algorithm"> + <param name="rt_estimate" value="false"/> + <param name="rt_pair_dist" value="-1.0"/> + <param name="rt_dev_low" value="0.4"/> + <param name="rt_dev_high" value="0.4"/> + <param name="mz_pair_dists" value="8.0"/> + <param name="mz_dev" value="0.1"/> + <param name="mrm" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureLinkerLabeled_2_input.featureXML"/> + <output name="out" file="FeatureLinkerLabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="algorithm"> + <param name="rt_estimate" value="true"/> + <param name="rt_pair_dist" value="-121.0382"/> + <param name="rt_dev_low" value="123.3965"/> + <param name="rt_dev_high" value="123.3965"/> + <param name="mz_pair_dists" value="4.0"/> + <param name="mz_dev" value="0.1"/> + <param name="mrm" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_FeatureLinkerUnlabeledKD"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> + <output name="out" file="FeatureLinkerUnlabeledKD_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="keep_subelements" value="false"/> + <section name="algorithm"> + <param name="mz_unit" value="Da"/> + <param name="nr_partitions" value="1"/> + <section name="warp"> + <param name="enabled" value="false"/> + <param name="rt_tol" value="100.0"/> + <param name="mz_tol" value="0.3"/> + <param name="max_pairwise_log_fc" value="0.5"/> + <param name="min_rel_cc_size" value="0.5"/> + <param name="max_nr_conflicts" value="0"/> + </section> + <section name="link"> + <param name="rt_tol" value="100.0"/> + <param name="mz_tol" value="0.3"/> + <param name="charge_merging" value="With_charge_zero"/> + <param name="adduct_merging" value="Any"/> + </section> + <section name="distance_RT"> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_MZ"> + <param name="exponent" value="2.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_intensity"> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + <param name="log_transform" value="enabled"/> + </section> + <section name="LOWESS"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureLinkerUnlabeledKD_1_output.consensusXML,FeatureLinkerUnlabeledKD_1_output_2.consensusXML"/> + <output name="out" file="FeatureLinkerUnlabeledKD_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="keep_subelements" value="true"/> + <section name="algorithm"> + <param name="mz_unit" value="Da"/> + <param name="nr_partitions" value="99999"/> + <section name="warp"> + <param name="enabled" value="false"/> + <param name="rt_tol" value="100.0"/> + <param name="mz_tol" value="0.3"/> + <param name="max_pairwise_log_fc" value="0.5"/> + <param name="min_rel_cc_size" value="0.5"/> + <param name="max_nr_conflicts" value="0"/> + </section> + <section name="link"> + <param name="rt_tol" value="100.0"/> + <param name="mz_tol" value="0.3"/> + <param name="charge_merging" value="With_charge_zero"/> + <param name="adduct_merging" value="Any"/> + </section> + <section name="distance_RT"> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_MZ"> + <param name="exponent" value="2.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_intensity"> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + <param name="log_transform" value="enabled"/> + </section> + <section name="LOWESS"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/> + <output name="out" file="FeatureLinkerUnlabeledKD_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="keep_subelements" value="false"/> + <section name="algorithm"> + <param name="mz_unit" value="Da"/> + <param name="nr_partitions" value="100"/> + <section name="warp"> + <param name="enabled" value="false"/> + <param name="rt_tol" value="100.0"/> + <param name="mz_tol" value="0.3"/> + <param name="max_pairwise_log_fc" value="0.5"/> + <param name="min_rel_cc_size" value="0.5"/> + <param name="max_nr_conflicts" value="0"/> + </section> + <section name="link"> + <param name="rt_tol" value="100.0"/> + <param name="mz_tol" value="0.3"/> + <param name="charge_merging" value="With_charge_zero"/> + <param name="adduct_merging" value="Any"/> + </section> + <section name="distance_RT"> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_MZ"> + <param name="exponent" value="2.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_intensity"> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + <param name="log_transform" value="enabled"/> + </section> + <section name="LOWESS"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/> + <output name="out" file="FeatureLinkerUnlabeledKD_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="keep_subelements" value="false"/> + <section name="algorithm"> + <param name="mz_unit" value="ppm"/> + <param name="nr_partitions" value="100"/> + <section name="warp"> + <param name="enabled" value="true"/> + <param name="rt_tol" value="100.0"/> + <param name="mz_tol" value="5.0"/> + <param name="max_pairwise_log_fc" value="0.5"/> + <param name="min_rel_cc_size" value="0.5"/> + <param name="max_nr_conflicts" value="0"/> + </section> + <section name="link"> + <param name="rt_tol" value="30.0"/> + <param name="mz_tol" value="10.0"/> + <param name="charge_merging" value="Identical"/> + <param name="adduct_merging" value="Any"/> + </section> + <section name="distance_RT"> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_MZ"> + <param name="exponent" value="2.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_intensity"> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + <param name="log_transform" value="enabled"/> + </section> + <section name="LOWESS"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/> + <output name="out" file="FeatureLinkerUnlabeledKD_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="keep_subelements" value="false"/> + <section name="algorithm"> + <param name="mz_unit" value="ppm"/> + <param name="nr_partitions" value="100"/> + <section name="warp"> + <param name="enabled" value="true"/> + <param name="rt_tol" value="100.0"/> + <param name="mz_tol" value="5.0"/> + <param name="max_pairwise_log_fc" value="0.5"/> + <param name="min_rel_cc_size" value="0.5"/> + <param name="max_nr_conflicts" value="0"/> + </section> + <section name="link"> + <param name="rt_tol" value="30.0"/> + <param name="mz_tol" value="10.0"/> + <param name="charge_merging" value="With_charge_zero"/> + <param name="adduct_merging" value="Any"/> + </section> + <section name="distance_RT"> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_MZ"> + <param name="exponent" value="2.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_intensity"> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + <param name="log_transform" value="enabled"/> + </section> + <section name="LOWESS"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/> + <output name="out" file="FeatureLinkerUnlabeledKD_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="keep_subelements" value="false"/> + <section name="algorithm"> + <param name="mz_unit" value="ppm"/> + <param name="nr_partitions" value="100"/> + <section name="warp"> + <param name="enabled" value="true"/> + <param name="rt_tol" value="100.0"/> + <param name="mz_tol" value="5.0"/> + <param name="max_pairwise_log_fc" value="0.5"/> + <param name="min_rel_cc_size" value="0.5"/> + <param name="max_nr_conflicts" value="0"/> + </section> + <section name="link"> + <param name="rt_tol" value="30.0"/> + <param name="mz_tol" value="10.0"/> + <param name="charge_merging" value="Any"/> + <param name="adduct_merging" value="With_unknown_adducts"/> + </section> + <section name="distance_RT"> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_MZ"> + <param name="exponent" value="2.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_intensity"> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + <param name="log_transform" value="enabled"/> + </section> + <section name="LOWESS"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/> + <output name="out" file="FeatureLinkerUnlabeledKD_7_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="keep_subelements" value="false"/> + <section name="algorithm"> + <param name="mz_unit" value="ppm"/> + <param name="nr_partitions" value="100"/> + <section name="warp"> + <param name="enabled" value="true"/> + <param name="rt_tol" value="100.0"/> + <param name="mz_tol" value="5.0"/> + <param name="max_pairwise_log_fc" value="0.5"/> + <param name="min_rel_cc_size" value="0.5"/> + <param name="max_nr_conflicts" value="0"/> + </section> + <section name="link"> + <param name="rt_tol" value="30.0"/> + <param name="mz_tol" value="10.0"/> + <param name="charge_merging" value="Any"/> + <param name="adduct_merging" value="Identical"/> + </section> + <section name="distance_RT"> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_MZ"> + <param name="exponent" value="2.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_intensity"> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + <param name="log_transform" value="enabled"/> + </section> + <section name="LOWESS"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_FeatureLinkerUnlabeledQT"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> + <output name="out" file="FeatureLinkerUnlabeledQT_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="keep_subelements" value="false"/> + <section name="algorithm"> + <param name="use_identifications" value="false"/> + <param name="nr_partitions" value="100"/> + <param name="ignore_charge" value="false"/> + <param name="ignore_adduct" value="true"/> + <section name="distance_RT"> + <param name="max_difference" value="100.0"/> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_MZ"> + <param name="max_difference" value="0.3"/> + <param name="unit" value="Da"/> + <param name="exponent" value="2.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_intensity"> + <param name="exponent" value="1.0"/> + <param name="weight" value="0.0"/> + <param name="log_transform" value="disabled"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureLinkerUnlabeledQT_1_output.consensusXML,FeatureLinkerUnlabeledQT_1_output_2.consensusXML"/> + <output name="out" file="FeatureLinkerUnlabeledQT_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="keep_subelements" value="true"/> + <section name="algorithm"> + <param name="use_identifications" value="false"/> + <param name="nr_partitions" value="100"/> + <param name="ignore_charge" value="false"/> + <param name="ignore_adduct" value="true"/> + <section name="distance_RT"> + <param name="max_difference" value="100.0"/> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_MZ"> + <param name="max_difference" value="0.3"/> + <param name="unit" value="Da"/> + <param name="exponent" value="2.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_intensity"> + <param name="exponent" value="1.0"/> + <param name="weight" value="0.0"/> + <param name="log_transform" value="disabled"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/> + <output name="out" file="FeatureLinkerUnlabeledQT_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="keep_subelements" value="false"/> + <section name="algorithm"> + <param name="use_identifications" value="false"/> + <param name="nr_partitions" value="99999"/> + <param name="ignore_charge" value="false"/> + <param name="ignore_adduct" value="true"/> + <section name="distance_RT"> + <param name="max_difference" value="100.0"/> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_MZ"> + <param name="max_difference" value="0.3"/> + <param name="unit" value="Da"/> + <param name="exponent" value="2.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_intensity"> + <param name="exponent" value="1.0"/> + <param name="weight" value="0.0"/> + <param name="log_transform" value="disabled"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> + <output name="out" file="FeatureLinkerUnlabeledQT_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="keep_subelements" value="false"/> + <section name="algorithm"> + <param name="use_identifications" value="true"/> + <param name="nr_partitions" value="100"/> + <param name="ignore_charge" value="false"/> + <param name="ignore_adduct" value="true"/> + <section name="distance_RT"> + <param name="max_difference" value="100.0"/> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_MZ"> + <param name="max_difference" value="0.3"/> + <param name="unit" value="Da"/> + <param name="exponent" value="2.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_intensity"> + <param name="exponent" value="1.0"/> + <param name="weight" value="0.0"/> + <param name="log_transform" value="disabled"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/> + <output name="out" file="FeatureLinkerUnlabeledQT_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="keep_subelements" value="false"/> + <section name="algorithm"> + <param name="use_identifications" value="false"/> + <param name="nr_partitions" value="100"/> + <param name="ignore_charge" value="false"/> + <param name="ignore_adduct" value="true"/> + <section name="distance_RT"> + <param name="max_difference" value="200.0"/> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_MZ"> + <param name="max_difference" value="0.3"/> + <param name="unit" value="Da"/> + <param name="exponent" value="2.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_intensity"> + <param name="exponent" value="1.0"/> + <param name="weight" value="0.0"/> + <param name="log_transform" value="disabled"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/> + <output name="out" file="FeatureLinkerUnlabeledQT_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="keep_subelements" value="false"/> + <section name="algorithm"> + <param name="use_identifications" value="true"/> + <param name="nr_partitions" value="100"/> + <param name="ignore_charge" value="false"/> + <param name="ignore_adduct" value="true"/> + <section name="distance_RT"> + <param name="max_difference" value="200.0"/> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_MZ"> + <param name="max_difference" value="0.3"/> + <param name="unit" value="Da"/> + <param name="exponent" value="2.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_intensity"> + <param name="exponent" value="1.0"/> + <param name="weight" value="0.0"/> + <param name="log_transform" value="disabled"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_FeatureLinkerUnlabeled"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> + <output name="out" file="FeatureLinkerUnlabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="keep_subelements" value="false"/> + <section name="algorithm"> + <param name="second_nearest_gap" value="2.0"/> + <param name="use_identifications" value="false"/> + <param name="ignore_charge" value="true"/> + <param name="ignore_adduct" value="true"/> + <section name="distance_RT"> + <param name="max_difference" value="200.0"/> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_MZ"> + <param name="max_difference" value="0.5"/> + <param name="unit" value="Da"/> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_intensity"> + <param name="exponent" value="1.0"/> + <param name="weight" value="0.0"/> + <param name="log_transform" value="disabled"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureLinkerUnlabeled_2_input1.featureXML,FeatureLinkerUnlabeled_2_input2.featureXML,FeatureLinkerUnlabeled_2_input3.featureXML"/> + <output name="out" file="FeatureLinkerUnlabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="keep_subelements" value="false"/> + <section name="algorithm"> + <param name="second_nearest_gap" value="2.0"/> + <param name="use_identifications" value="false"/> + <param name="ignore_charge" value="false"/> + <param name="ignore_adduct" value="true"/> + <section name="distance_RT"> + <param name="max_difference" value="100.0"/> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_MZ"> + <param name="max_difference" value="0.3"/> + <param name="unit" value="Da"/> + <param name="exponent" value="2.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_intensity"> + <param name="exponent" value="1.0"/> + <param name="weight" value="0.5"/> + <param name="log_transform" value="disabled"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureLinkerUnlabeled_3_input1.featureXML,FeatureLinkerUnlabeled_3_input2.featureXML"/> + <output name="out" file="FeatureLinkerUnlabeled_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="keep_subelements" value="false"/> + <section name="algorithm"> + <param name="second_nearest_gap" value="1.5"/> + <param name="use_identifications" value="false"/> + <param name="ignore_charge" value="true"/> + <param name="ignore_adduct" value="true"/> + <section name="distance_RT"> + <param name="max_difference" value="30.0"/> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_MZ"> + <param name="max_difference" value="0.3"/> + <param name="unit" value="Da"/> + <param name="exponent" value="2.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_intensity"> + <param name="exponent" value="1.0"/> + <param name="weight" value="0.0"/> + <param name="log_transform" value="disabled"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> + <output name="out" file="FeatureLinkerUnlabeled_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="keep_subelements" value="false"/> + <section name="algorithm"> + <param name="second_nearest_gap" value="2.0"/> + <param name="use_identifications" value="true"/> + <param name="ignore_charge" value="true"/> + <param name="ignore_adduct" value="true"/> + <section name="distance_RT"> + <param name="max_difference" value="200.0"/> + <param name="exponent" value="2.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_MZ"> + <param name="max_difference" value="0.5"/> + <param name="unit" value="Da"/> + <param name="exponent" value="2.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_intensity"> + <param name="exponent" value="1.0"/> + <param name="weight" value="0.0"/> + <param name="log_transform" value="disabled"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_FFEval"> +</xml> + <xml name="autotest_FidoAdapter"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="keep_zero_group" value="false"/> + <param name="accuracy" value=""/> + <param name="log2_states_precalc" value="0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FidoAdapter_1_input.idXML"/> + <output name="out" file="FidoAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="separate_runs" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="no_cleanup" value="false"/> + <param name="all_PSMs" value="false"/> + <param name="group_level" value="false"/> + <param name="log2_states" value="0"/> + <section name="prob"> + <param name="protein" value="0.0"/> + <param name="peptide" value="0.0"/> + <param name="spurious" value="0.0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="keep_zero_group" value="false"/> + <param name="accuracy" value=""/> + <param name="log2_states_precalc" value="0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FidoAdapter_1_input.idXML"/> + <output name="out" file="FidoAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="separate_runs" value="true"/> + <param name="greedy_group_resolution" value="false"/> + <param name="no_cleanup" value="false"/> + <param name="all_PSMs" value="false"/> + <param name="group_level" value="false"/> + <param name="log2_states" value="0"/> + <section name="prob"> + <param name="protein" value="0.0"/> + <param name="peptide" value="0.0"/> + <param name="spurious" value="0.0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="keep_zero_group" value="false"/> + <param name="accuracy" value=""/> + <param name="log2_states_precalc" value="0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FidoAdapter_1_input.idXML"/> + <output name="out" file="FidoAdapter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="separate_runs" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="no_cleanup" value="false"/> + <param name="all_PSMs" value="true"/> + <param name="group_level" value="true"/> + <param name="log2_states" value="0"/> + <section name="prob"> + <param name="protein" value="0.0"/> + <param name="peptide" value="0.0"/> + <param name="spurious" value="0.0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="keep_zero_group" value="false"/> + <param name="accuracy" value=""/> + <param name="log2_states_precalc" value="0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FidoAdapter_4_input.idXML"/> + <output name="out" file="FidoAdapter_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="separate_runs" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="no_cleanup" value="false"/> + <param name="all_PSMs" value="false"/> + <param name="group_level" value="false"/> + <param name="log2_states" value="0"/> + <section name="prob"> + <param name="protein" value="0.0"/> + <param name="peptide" value="0.0"/> + <param name="spurious" value="0.0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="keep_zero_group" value="false"/> + <param name="accuracy" value=""/> + <param name="log2_states_precalc" value="0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FidoAdapter_5_input.idXML"/> + <output name="out" file="FidoAdapter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="separate_runs" value="false"/> + <param name="greedy_group_resolution" value="true"/> + <param name="no_cleanup" value="false"/> + <param name="all_PSMs" value="false"/> + <param name="group_level" value="false"/> + <param name="log2_states" value="0"/> + <section name="prob"> + <param name="protein" value="0.0"/> + <param name="peptide" value="0.0"/> + <param name="spurious" value="0.0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="keep_zero_group" value="false"/> + <param name="accuracy" value=""/> + <param name="log2_states_precalc" value="0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FidoAdapter_1_input.idXML"/> + <output name="out" file="FidoAdapter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="separate_runs" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="no_cleanup" value="false"/> + <param name="all_PSMs" value="false"/> + <param name="group_level" value="false"/> + <param name="log2_states" value="0"/> + <section name="prob"> + <param name="protein" value="0.9"/> + <param name="peptide" value="0.01"/> + <param name="spurious" value="0.0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_FileConverter"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <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"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_2_input.someInputDTA2D"/> + <output name="out" file="FileConverter_2_output.mzML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_3_input.featureXML"/> + <output name="out" file="FileConverter_3_output.mzML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_4_input.mzXML"/> + <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_5_input.mzML"/> + <output name="out" file="FileConverter_5_output.mzXML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_6_input.mzML"/> + <output name="out" file="FileConverter_6_output.mzXML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_7_input.consensusXML"/> + <output name="out" file="FileConverter_7_output.featureXML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_8_input.mzML"/> + <output name="out" file="FileConverter_8_output.mzData" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_9_input.consensusXML"/> + <output name="out" file="FileConverter_9_output.featureXML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_10_input.edta" ftype="edta"/> + <output name="out" file="FileConverter_10_output.featureXML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_11_input.peplist"/> + <output name="out" file="FileConverter_11_output.featureXML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_12_input.peptides.tsv" ftype="tabular"/> + <output name="out" file="FileConverter_12_output.featureXML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_13_input.peptides.kroenik"/> + <output name="out" file="FileConverter_13_output.featureXML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_9_output.featureXML"/> + <output name="out" file="FileConverter_14_output.consensusXML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_10_input.edta" ftype="edta"/> + <output name="out" file="FileConverter_15_output.consensusXML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_16_input.edta" ftype="edta"/> + <output name="out" file="FileConverter_16_output.consensusXML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_17_input.consensusXML"/> + <output name="out" file="FileConverter_17.csv" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_17_input.consensusXML"/> + <output name="out" file="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_1_input.mzML"/> + <output name="out" file="FileConverter_19_output.mzML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_20_input.featureXML"/> + <output name="out" file="FileConverter_20_output.featureXML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_4_input.mzXML"/> + <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_23_input.mzML"/> + <output name="out" file="FileConverter_23_output.mzML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_1_input.mzML"/> + <output name="out" file="FileConverter_24_output.mzML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_1_input.mzML"/> + <output name="out" file="FileConverter_25_output.mzML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_1_input.mzML"/> + <output name="out" file="FileConverter_26_output.mzXML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_26_output.mzXML"/> + <output name="out" file="FileConverter_26-2_output.mzXML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="true"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_27_input.mzML"/> + <output name="out" file="FileConverter_27_output.mzML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="true"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_28_input.mzML"/> + <output name="out" file="FileConverter_28_output.mzML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> + <output name="out" file="FileConverter_29_output.mzML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_29_output.mzML"/> + <output name="out" file="FileConverter_29.back.tmp" compare="sim_size" delta="5700"/> + <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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" value="false"/> + <param name="change_im_format" value="multiple"/> + <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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_30_input.mzML"/> + <output name="out" file="FileConverter_30_output.mzML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" value="false"/> + <param name="change_im_format" value="single"/> + <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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_30_output.mzML"/> + <output name="out" file="FileConverter_31_output.mzML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileConverter_32_input.mzML"/> + <output name="out" file="FileConverter_32_output.mzML" compare="sim_size" delta="5700" 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> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <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="convert_to_chromatograms" value="false"/> + <param name="force_TPP_compatibility" 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="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ginkgotoxin-ms-switching.raw"/> + <output name="out" file="ginkgotoxin-ms-switching_out_tmp.mzML" compare="sim_size" delta="5700" 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> + </test> + </xml> + <xml name="autotest_FileFilter"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_1_input.mzML"/> + <output name="out" file="FileFilter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="rt" value=":30"/> + <param name="mz" value=":1000"/> + <param name="int" value=":20000"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_1_input.mzML"/> + <output name="out" file="FileFilter_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="rt" value="30:"/> + <param name="mz" value="1000:"/> + <param name="int" value="100:"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_1_input.mzML"/> + <output name="out" file="FileFilter_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="2"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_4_input.mzML"/> + <output name="out" file="FileFilter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="true"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_5_input.featureXML"/> + <output name="out" file="FileFilter_5_out.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="out_type" value="featureXML"/> + <param name="rt" value=":1000"/> + <param name="mz" value=":480"/> + <param name="int" value=":79000"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":0.6"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":3"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_5_input.featureXML"/> + <output name="out" file="FileFilter_6_out.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="out_type" value="featureXML"/> + <param name="rt" value="1000:"/> + <param name="mz" value="440:"/> + <param name="int" value="70000:"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value="0.51:"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value="3:"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_7_input.mzML"/> + <output name="out" file="FileFilter_7_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value="7000:"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_8_input.consensusXML"/> + <output name="out" file="FileFilter_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="out_type" value="consensusXML"/> + <param name="rt" value="600:1400"/> + <param name="mz" value="700:2300"/> + <param name="int" value="1100:6000"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_9_input.mzML"/> + <output name="out" file="FileFilter_9_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value="SelectedIonMonitoring"/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_10_input.mzML"/> + <output name="out" file="FileFilter_10_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value="Collision-induced dissociation"/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_11_input.mzML"/> + <output name="out" file="FileFilter_11_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value="Plasma desorption"/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_12_input.mzML"/> + <output name="out" file="FileFilter_12_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="true"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_13_input.consensusXML"/> + <output name="out" file="FileFilter_13_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="out_type" value="featureXML"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value="2"/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_14_input.consensusXML"/> + <output name="out" file="FileFilter_14_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="out_type" value="consensusXML"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value="0 2"/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_15_input.featureXML"/> + <output name="out" file="FileFilter_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="out_type" value="featurexml"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""Oxidation""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="true"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_15_input.featureXML"/> + <output name="out" file="FileFilter_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="out_type" value="featurexml"/> + <param name="rt" value="3000:4000"/> + <param name="mz" value="400:600"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""Oxidation""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="true"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_15_input.featureXML"/> + <output name="out" file="FileFilter_17_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="out_type" value="featurexml"/> + <param name="rt" value="3000:4000"/> + <param name="mz" value="400:600"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="true"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_18_input.consensusXML"/> + <output name="out" file="FileFilter_18_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="out_type" value="consensusxml"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""Oxidation""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="true"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_18_input.consensusXML"/> + <output name="out" file="FileFilter_19_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="out_type" value="consensusxml"/> + <param name="rt" value="3000:4000"/> + <param name="mz" value="400:600"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="true"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_15_input.featureXML"/> + <output name="out" file="FileFilter_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="out_type" value="featurexml"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""YDL217C""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="true"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_15_input.featureXML"/> + <output name="out" file="FileFilter_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="out_type" value="featurexml"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="true"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="true"/> + <param name="remove_unassigned_ids" value="true"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_22_input.consensusXML"/> + <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="out_type" value="consensusxml"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""distinct_charges" "gt" "1,2""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_22_input.consensusXML"/> + <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="out_type" value="consensusxml"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""distinct_charges_size" "gt" "2""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_22_input.consensusXML"/> + <output name="out" file="FileFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="out_type" value="consensusxml"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""DOESNOTEXIST" "lt" "whatever""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_25_input.mzML.gz"/> + <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzml"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="blacklist" value="FileFilter_25_input.idXML"/> + <param name="rt" value="1.0"/> + <param name="mz" value="0.05"/> + <param name="blacklist_imperfect" value="true"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_25_input.mzML.gz"/> + <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzml"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="blacklist" value="FileFilter_25_input.idXML"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="true"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_28_input.mzML.gz"/> + <output name="out" file="FileFilter_28_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzml"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value="832:836"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="2"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_28_input.mzML.gz"/> + <output name="out" file="FileFilter_29_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzml"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value="832:836"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_28_input.mzML.gz"/> + <output name="out" file="FileFilter_30_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzml"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value="832:836"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_31_34_input.mzML"/> + <output name="out" file="FileFilter_31_remove_collision_energy.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzml"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":2"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_31_34_input.mzML"/> + <output name="out" file="FileFilter_32_select_collision_energy.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzml"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":2"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_31_34_input.mzML"/> + <output name="out" file="FileFilter_33_remove_isolation_window.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzml"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":35"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_31_34_input.mzML"/> + <output name="out" file="FileFilter_34_select_isolation_window.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzml"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":35"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_1_input.mzML"/> + <output name="out" file="FileFilter_35_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_1_input.mzML"/> + <output name="out" file="FileFilter_36_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="false"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_1_input.mzML"/> + <output name="out" file="FileFilter_37_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="linear"/> + <param name="lossy_mass_accuracy" value="0.0001"/> + <param name="intensity" value="slof"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_1_input.mzML"/> + <output name="out" file="FileFilter_38_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="linear"/> + <param name="lossy_mass_accuracy" value="0.0001"/> + <param name="intensity" value="pic"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_40_input.mzML"/> + <output name="out" file="FileFilter_40_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value="positive"/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_40_input.mzML"/> + <output name="out" file="FileFilter_41_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value="negative"/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_40_input.mzML"/> + <output name="out" file="FileFilter_42_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_43_input.mzML"/> + <output name="out" file="FileFilter_43.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_43.tmp.mzML"/> + <output name="out" file="FileFilter_43.dummy.tmp" compare="sim_size" delta="5700"/> + <param name="out_type" value="mzML"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_44_input.mzML"/> + <output name="out" file="FileFilter_44_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzML"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_45_input.featureXML"/> + <output name="out" file="FileFilter_45_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="out_type" value="featurexml"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""YSFS" "STLIPPPSK(Label:13C(6)15N(2))""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_46_input.featureXML"/> + <output name="out" file="FileFilter_46_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="out_type" value="featurexml"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""YSFS" "STLIPPPSK(Label:13C(6)15N(2))""/> + <param name="sequence_comparison_method" value="exact"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_47_input.mzML"/> + <output name="out" file="FileFilter_47_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzml"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="file" value="FileFilter_47_input_select.mzML"/> + <param name="similarity_threshold" value="0.9"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_47_input.mzML"/> + <output name="out" file="FileFilter_48_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzml"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="false"/> + <section name="numpress"> + <param name="masstime" value="none"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="none"/> + <param name="float_da" value="none"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="file" value="FileFilter_47_input_select.mzML"/> + <param name="similarity_threshold" value="0.9"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="false"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_49_input.mzML"/> + <output name="out" file="FileFilter_49_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzml"/> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="int" value=":"/> + <param name="sort" value="false"/> + <section name="peak_options"> + <param name="sn" value="0.0"/> + <param name="rm_pc_charge" value=""/> + <param name="pc_mz_range" value=":"/> + <param name="pc_mz_list" value=""/> + <param name="level" value="1 2 3"/> + <param name="sort_peaks" value="false"/> + <param name="no_chromatograms" value="false"/> + <param name="remove_chromatograms" value="false"/> + <param name="remove_empty" value="false"/> + <param name="mz_precision" value="64"/> + <param name="int_precision" value="32"/> + <param name="indexed_file" value="true"/> + <param name="zlib_compression" value="true"/> + <section name="numpress"> + <param name="masstime" value="linear"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="intensity" value="pic"/> + <param name="float_da" value="slof"/> + </section> + </section> + <section name="spectra"> + <param name="remove_zoom" value="false"/> + <param name="remove_mode" value=""/> + <param name="remove_activation" value=""/> + <param name="remove_collision_energy" value=":"/> + <param name="remove_isolation_window_width" value=":"/> + <param name="select_zoom" value="false"/> + <param name="select_mode" value=""/> + <param name="select_activation" value=""/> + <param name="select_collision_energy" value=":"/> + <param name="select_isolation_window_width" value=":"/> + <param name="select_polarity" value=""/> + <section name="blackorwhitelist"> + <param name="similarity_threshold" value="-1.0"/> + <param name="rt" value="0.01"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + <param name="blacklist" value="true"/> + </section> + </section> + <section name="feature"> + <param name="q" value=":"/> + </section> + <section name="consensus"> + <param name="map" value=""/> + <param name="map_and" value="false"/> + <section name="blackorwhitelist"> + <param name="blacklist" value="true"/> + <param name="maps" value=""/> + <param name="rt" value="60.0"/> + <param name="mz" value="0.01"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + </section> + <section name="f_and_c"> + <param name="charge" value=":"/> + <param name="size" value=":"/> + <param name="remove_meta" value=""/> + </section> + <section name="id"> + <param name="remove_clashes" value="false"/> + <param name="keep_best_score_id" value="false"/> + <param name="sequences_whitelist" value=""/> + <param name="sequence_comparison_method" value="substring"/> + <param name="accessions_whitelist" value=""/> + <param name="remove_annotated_features" value="false"/> + <param name="remove_unannotated_features" value="false"/> + <param name="remove_unassigned_ids" value="false"/> + <param name="rt" value="0.1"/> + <param name="mz" value="0.001"/> + <param name="blacklist_imperfect" value="false"/> + </section> + <section name="algorithm"> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_FileInfo"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileInfo_1_input.dta" ftype="dta"/> + <output name="out" file="FileInfo_1_output.txt" compare="sim_size" delta="5700" ftype="txt"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileInfo_2_input.dta2d" ftype="dta2d"/> + <output name="out" file="FileInfo_2_output.txt" compare="sim_size" delta="5700" ftype="txt"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileInfo_3_input.featureXML"/> + <output name="out" file="FileInfo_3_output.txt" compare="sim_size" delta="5700" ftype="txt"/> + <param name="m" value="true"/> + <param name="p" value="true"/> + <param name="s" value="true"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileInfo_4_input.mzXML"/> + <output name="out" file="FileInfo_4_output.txt" compare="sim_size" delta="5700" ftype="txt"/> + <param name="m" value="true"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileInfo_5_input.mzDat"/> + <output name="out" file="FileInfo_5_output.txt" compare="sim_size" delta="5700" ftype="txt"/> + <param name="m" value="true"/> + <param name="p" value="false"/> + <param name="s" value="true"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileInfo_6_input.mzData"/> + <output name="out" file="FileInfo_6_output.txt" compare="sim_size" delta="5700" ftype="txt"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="true"/> + <param name="d" value="true"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileInfo_7_input.consensusXML"/> + <output name="out" file="FileInfo_7_output.txt" compare="sim_size" delta="5700" ftype="txt"/> + <param name="m" value="true"/> + <param name="p" value="true"/> + <param name="s" value="true"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileInfo_9_input.mzML"/> + <output name="out" file="FileInfo_9_output.txt" compare="sim_size" delta="5700" ftype="txt"/> + <param name="m" value="true"/> + <param name="p" value="true"/> + <param name="s" value="true"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileInfo_10_input.idXML"/> + <output name="out" file="FileInfo_10_output.txt" compare="sim_size" delta="5700" ftype="txt"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileInfo_12_input.mzML"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileInfo_13_input.consensusXML"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileInfo_14_input.mzid"/> + <output name="out" file="FileInfo_14_output.txt" compare="sim_size" delta="5700" ftype="txt"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="true"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileInfo_15_input.mzid"/> + <output name="out" file="FileInfo_15_output.txt" compare="sim_size" delta="5700" ftype="txt"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="true"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileInfo_16_input.trafoXML"/> + <output name="out" file="FileInfo_16_output.txt" compare="sim_size" delta="5700" ftype="txt"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileInfo_17_input.fasta"/> + <output name="out" file="FileInfo_17_output.txt" compare="sim_size" delta="5700" ftype="txt"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileInfo_18_input.fasta"/> + <output name="out" file="FileInfo_18_output.txt" compare="sim_size" delta="5700" ftype="txt"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_FileMerger"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileMerger_2_input1.dta,FileMerger_2_input2.dta" ftype="dta"/> + <param name="out_type" value="mzML"/> + <output name="out" file="FileMerger_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="annotate_file_origin" value="false"/> + <param name="append_method" value="append_rows"/> + <section name="rt_concat"> + <param name="gap" value="0.0"/> + </section> + <section name="raw"> + <param name="rt_auto" value="false"/> + <param name="rt_custom" value="5.0 10.0"/> + <param name="rt_filename" value="false"/> + <param name="ms_level" value="0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileMerger_3_input1.dta,FileMerger_3_input2.dta" ftype="dta"/> + <param name="out_type" value="mzML"/> + <output name="out" file="FileMerger_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="annotate_file_origin" value="false"/> + <param name="append_method" value="append_rows"/> + <section name="rt_concat"> + <param name="gap" value="0.0"/> + </section> + <section name="raw"> + <param name="rt_auto" value="true"/> + <param name="rt_custom" value=""/> + <param name="rt_filename" value="false"/> + <param name="ms_level" value="0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileMerger_4_input1.dta2d,FileMerger_4_input2.dta2d" ftype="dta2d"/> + <param name="out_type" value="mzML"/> + <output name="out" file="FileMerger_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="annotate_file_origin" value="false"/> + <param name="append_method" value="append_rows"/> + <section name="rt_concat"> + <param name="gap" value="0.0"/> + </section> + <section name="raw"> + <param name="rt_auto" value="false"/> + <param name="rt_custom" value=""/> + <param name="rt_filename" value="false"/> + <param name="ms_level" value="0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileMerger_5_input_rt1023.331.dta,FileMerger_5_input_rt2044.334.dta,FileMerger_5_input_rt889.32.dta" ftype="dta"/> + <param name="out_type" value="mzML"/> + <output name="out" file="FileMerger_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="annotate_file_origin" value="false"/> + <param name="append_method" value="append_rows"/> + <section name="rt_concat"> + <param name="gap" value="0.0"/> + </section> + <section name="raw"> + <param name="rt_auto" value="false"/> + <param name="rt_custom" value=""/> + <param name="rt_filename" value="true"/> + <param name="ms_level" value="2"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileMerger_6_input1.mzML,FileMerger_6_input2.mzML"/> + <param name="out_type" value="mzML"/> + <output name="out" file="FileMerger_6_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="annotate_file_origin" value="false"/> + <param name="append_method" value="append_rows"/> + <section name="rt_concat"> + <param name="gap" value="0.0"/> + </section> + <section name="raw"> + <param name="rt_auto" value="false"/> + <param name="rt_custom" value=""/> + <param name="rt_filename" value="false"/> + <param name="ms_level" value="0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileMerger_7_input1.featureXML,FileMerger_7_input2.featureXML"/> + <param name="out_type" value="featureXML"/> + <output name="out" file="FileMerger_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="annotate_file_origin" value="false"/> + <param name="append_method" value="append_rows"/> + <section name="rt_concat"> + <param name="gap" value="0.0"/> + </section> + <section name="raw"> + <param name="rt_auto" value="false"/> + <param name="rt_custom" value=""/> + <param name="rt_filename" value="false"/> + <param name="ms_level" value="0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/> + <param name="out_type" value="consensusXML"/> + <output name="out" file="FileMerger_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="annotate_file_origin" value="false"/> + <param name="append_method" value="append_rows"/> + <section name="rt_concat"> + <param name="gap" value="0.0"/> + </section> + <section name="raw"> + <param name="rt_auto" value="false"/> + <param name="rt_custom" value=""/> + <param name="rt_filename" value="false"/> + <param name="ms_level" value="0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileMerger_9_input1.traML,FileMerger_9_input2.traML"/> + <param name="out_type" value="traML"/> + <output name="out" file="FileMerger_9_output.traML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="annotate_file_origin" value="false"/> + <param name="append_method" value="append_rows"/> + <section name="rt_concat"> + <param name="gap" value="0.0"/> + </section> + <section name="raw"> + <param name="rt_auto" value="false"/> + <param name="rt_custom" value=""/> + <param name="rt_filename" value="false"/> + <param name="ms_level" value="0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileMerger_6_input2.mzML,FileMerger_6_input2_2.mzML"/> + <param name="out_type" value="mzML"/> + <output name="out" file="FileMerger_10_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="annotate_file_origin" value="false"/> + <param name="append_method" value="append_rows"/> + <section name="rt_concat"> + <param name="gap" value="10.0"/> + </section> + <output_collection name="rt_concat_trafo_out" count="2"/> + <section name="raw"> + <param name="rt_auto" value="false"/> + <param name="rt_custom" value=""/> + <param name="rt_filename" value="false"/> + <param name="ms_level" value="0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/> + <param name="out_type" value="consensusXML"/> + <output name="out" file="FileMerger_11_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="annotate_file_origin" value="false"/> + <param name="append_method" value="append_cols"/> + <section name="rt_concat"> + <param name="gap" value="0.0"/> + </section> + <section name="raw"> + <param name="rt_auto" value="false"/> + <param name="rt_custom" value=""/> + <param name="rt_filename" value="false"/> + <param name="ms_level" value="0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_FuzzyDiff"> + <test expect_num_outputs="1"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="whitelist" value=""<?xml-stylesheet""/> + <param name="matched_whitelist" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in1" value="FuzzyDiff_3_in1.featureXML"/> + <param name="in2" value="FuzzyDiff_3_in2.featureXML"/> + <param name="ratio" value="1.01"/> + <param name="absdiff" value="0.01"/> + <param name="verbose" value="1"/> + <param name="tab_width" value="8"/> + <param name="first_column" value="1"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_GNPSExport"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in_cm" value="GNPSExport_single.consensusXML"/> + <param name="in_mzml" value="GNPSExport_mz1.mzML"/> + <output name="out" file="GNPSExport_1_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/> + <param name="output_type" value="full_spectra"/> + <param name="precursor_mz_tolerance" value="0.0001"/> + <param name="precursor_rt_tolerance" value="5.0"/> + <section name="merged_spectra"> + <param name="cos_similarity" value="0.95"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in_cm" value="GNPSExport_single.consensusXML"/> + <param name="in_mzml" value="GNPSExport_mz1.mzML"/> + <output name="out" file="GNPSExport_2_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/> + <param name="output_type" value="merged_spectra"/> + <param name="precursor_mz_tolerance" value="0.0001"/> + <param name="precursor_rt_tolerance" value="5.0"/> + <section name="merged_spectra"> + <param name="cos_similarity" value="0.95"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in_cm" value="GNPSExport_merged.consensusXML"/> + <param name="in_mzml" value="GNPSExport_mz1.mzML,GNPSExport_mz2.mzML"/> + <output name="out" file="GNPSExport_3_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/> + <param name="output_type" value="full_spectra"/> + <param name="precursor_mz_tolerance" value="0.0001"/> + <param name="precursor_rt_tolerance" value="5.0"/> + <section name="merged_spectra"> + <param name="cos_similarity" value="0.95"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in_cm" value="GNPSExport_merged.consensusXML"/> + <param name="in_mzml" value="GNPSExport_mz1.mzML,GNPSExport_mz2.mzML"/> + <output name="out" file="GNPSExport_4_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/> + <param name="output_type" value="full_spectra"/> + <param name="precursor_mz_tolerance" value="0.0001"/> + <param name="precursor_rt_tolerance" value="5.0"/> + <section name="merged_spectra"> + <param name="cos_similarity" value="0.95"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_HighResPrecursorMassCorrector"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.mzML"/> + <output name="out" file="HighResPrecursorMassCorrector_2860_1103_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="feature"> + <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.featureXML"/> + <param name="mz_tolerance" value="5.0"/> + <param name="mz_tolerance_unit" value="ppm"/> + <param name="rt_tolerance" value="0.0"/> + <param name="max_trace" value="2"/> + <param name="believe_charge" value="false"/> + <param name="keep_original" value="false"/> + <param name="assign_all_matching" value="false"/> + </section> + <section name="nearest_peak"> + <param name="mz_tolerance" value="0.0"/> + <param name="mz_tolerance_unit" value="ppm"/> + </section> + <section name="highest_intensity_peak"> + <param name="mz_tolerance" value="0.0"/> + <param name="mz_tolerance_unit" value="ppm"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.mzML"/> + <output name="out" file="HighResPrecursorMassCorrector_1035_1178_4_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="feature"> + <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.featureXML"/> + <param name="mz_tolerance" value="10.0"/> + <param name="mz_tolerance_unit" value="ppm"/> + <param name="rt_tolerance" value="0.0"/> + <param name="max_trace" value="4"/> + <param name="believe_charge" value="false"/> + <param name="keep_original" value="false"/> + <param name="assign_all_matching" value="false"/> + </section> + <section name="nearest_peak"> + <param name="mz_tolerance" value="0.0"/> + <param name="mz_tolerance_unit" value="ppm"/> + </section> + <section name="highest_intensity_peak"> + <param name="mz_tolerance" value="0.0"/> + <param name="mz_tolerance_unit" value="ppm"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.mzML"/> + <output name="out" file="HighResPrecursorMassCorrector_2538_1091_2_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="feature"> + <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.featureXML"/> + <param name="mz_tolerance" value="5.0"/> + <param name="mz_tolerance_unit" value="ppm"/> + <param name="rt_tolerance" value="0.0"/> + <param name="max_trace" value="2"/> + <param name="believe_charge" value="false"/> + <param name="keep_original" value="false"/> + <param name="assign_all_matching" value="false"/> + </section> + <section name="nearest_peak"> + <param name="mz_tolerance" value="0.0"/> + <param name="mz_tolerance_unit" value="ppm"/> + </section> + <section name="highest_intensity_peak"> + <param name="mz_tolerance" value="0.0"/> + <param name="mz_tolerance_unit" value="ppm"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.mzML"/> + <output name="out" file="HighResPrecursorMassCorrector_2810_1091_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="feature"> + <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.featureXML"/> + <param name="mz_tolerance" value="5.0"/> + <param name="mz_tolerance_unit" value="ppm"/> + <param name="rt_tolerance" value="0.0"/> + <param name="max_trace" value="2"/> + <param name="believe_charge" value="false"/> + <param name="keep_original" value="false"/> + <param name="assign_all_matching" value="false"/> + </section> + <section name="nearest_peak"> + <param name="mz_tolerance" value="0.0"/> + <param name="mz_tolerance_unit" value="ppm"/> + </section> + <section name="highest_intensity_peak"> + <param name="mz_tolerance" value="0.0"/> + <param name="mz_tolerance_unit" value="ppm"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.mzML"/> + <output name="out" file="HighResPrecursorMassCorrector_3070_1191_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="feature"> + <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.featureXML"/> + <param name="mz_tolerance" value="5.0"/> + <param name="mz_tolerance_unit" value="ppm"/> + <param name="rt_tolerance" value="0.0"/> + <param name="max_trace" value="2"/> + <param name="believe_charge" value="false"/> + <param name="keep_original" value="false"/> + <param name="assign_all_matching" value="false"/> + </section> + <section name="nearest_peak"> + <param name="mz_tolerance" value="0.0"/> + <param name="mz_tolerance_unit" value="ppm"/> + </section> + <section name="highest_intensity_peak"> + <param name="mz_tolerance" value="0.0"/> + <param name="mz_tolerance_unit" value="ppm"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="HighResPrecursorMassCorrector_6.mzML"/> + <output name="out" file="HighResPrecursorMassCorrector_6_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="feature"> + <param name="mz_tolerance" value="5.0"/> + <param name="mz_tolerance_unit" value="ppm"/> + <param name="rt_tolerance" value="0.0"/> + <param name="max_trace" value="2"/> + <param name="believe_charge" value="false"/> + <param name="keep_original" value="false"/> + <param name="assign_all_matching" value="false"/> + </section> + <section name="nearest_peak"> + <param name="mz_tolerance" value="0.0"/> + <param name="mz_tolerance_unit" value="ppm"/> + </section> + <section name="highest_intensity_peak"> + <param name="mz_tolerance" value="0.2"/> + <param name="mz_tolerance_unit" value="ppm"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_IDConflictResolver"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDConflictResolver_1_input.featureXML"/> + <output name="out" file="IDConflictResolver_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="resolve_between_features" value="off"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDConflictResolver_2_input.consensusXML"/> + <output name="out" file="IDConflictResolver_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="resolve_between_features" value="off"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDConflictResolver_3_input.consensusXML"/> + <output name="out" file="IDConflictResolver_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="resolve_between_features" value="off"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDConflictResolver_4_input.featureXML"/> + <output name="out" file="IDConflictResolver_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="resolve_between_features" value="highest_intensity"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_IDExtractor"> +</xml> + <xml name="autotest_IDFileConverter"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_1_input1.mascotXML"/> + <output name="out" file="IDFileConverter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="mz_file" value="IDFileConverter_1_input2.mzML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PepXMLFile_test.pepxml"/> + <output name="out" file="IDFileConverter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="mz_file" value="PepXMLFile_test.mzML"/> + <param name="mz_name" value="PepXMLFile_test"/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_3_input.protXML"/> + <output name="out" file="IDFileConverter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value="scan=(?<SCAN>\d+)"/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_1_input1.mascotXML"/> + <output name="out" file="IDFileConverter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="mz_file" value="IDFileConverter_1_input2.mzML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_6_input1.pepXML"/> + <output name="out" file="IDFileConverter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="mz_file" value="IDFileConverter_1_input2.mzML"/> + <param name="mz_name" value="F025589.dat.mzML"/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_7_input1.xml"/> + <output name="out" file="IDFileConverter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_8_input.mzid"/> + <output name="out" file="IDFileConverter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_9_input.idXML"/> + <output name="out" file="IDFileConverter_9_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/> + <param name="out_type" value="mzid"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_10_input.pepXML"/> + <output name="out" file="IDFileConverter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_11_input.tsv" ftype="tabular"/> + <output name="out" file="IDFileConverter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_12_input.psms"/> + <output name="out" file="IDFileConverter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_12_input.psms"/> + <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="PEP"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_12_input.psms"/> + <output name="out" file="IDFileConverter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="score"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MSGFPlusAdapter_1_out.mzid"/> + <output name="out" file="IDFileConverter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="mz_file" value="spectra.mzML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_16_input.pepXML"/> + <output name="out" file="IDFileConverter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_17_input.idXML"/> + <output name="out" file="IDFileConverter_17_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> + <param name="out_type" value="pepXML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_18_input.idXML"/> + <output name="out" file="IDFileConverter_18_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> + <param name="out_type" value="pepXML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_19_input.idXML"/> + <output name="out" file="IDFileConverter_19_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> + <param name="out_type" value="pepXML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_20_input.idXML"/> + <output name="out" file="IDFileConverter_20_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> + <param name="out_type" value="pepXML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_21_input.idXML"/> + <output name="out" file="IDFileConverter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="mz_file" value="IDMapper_4_input.mzML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.01"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MSGFPlusAdapter_1_out.mzid"/> + <output name="out" file="IDFileConverter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="mz_file" value="spectra.mzML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_23_input.mzid"/> + <output name="out" file="IDFileConverter_23_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_24_input.pep.xml"/> + <output name="out" file="IDFileConverter_24_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_25_input.idXML"/> + <output name="out" file="IDFileConverter_25_output.pep.xml" compare="sim_size" delta="5700" ftype="pepxml"/> + <param name="out_type" value="pepXML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_26_input.mzid"/> + <output name="out" file="IDFileConverter_26_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_27_input.idXML"/> + <output name="out" file="IDFileConverter_27_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/> + <param name="out_type" value="FASTA"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="-1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_27_input.idXML"/> + <output name="out" file="IDFileConverter_28_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/> + <param name="out_type" value="FASTA"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="true"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_27_input.idXML"/> + <output name="out" file="IDFileConverter_29_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/> + <param name="out_type" value="FASTA"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="true"/> + <param name="number_of_hits" value="2"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_27_input.idXML"/> + <output name="out" file="IDFileConverter_30_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/> + <param name="out_type" value="FASTA"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_proteins_per_peptide" value="false"/> + <param name="scan_regex" value=""/> + <param name="no_spectra_data_override" value="false"/> + <param name="no_spectra_references_override" value="false"/> + <param name="add_ionmatch_annotation" value="0.0"/> + <param name="concatenate_peptides" value="false"/> + <param name="number_of_hits" value="1"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_31_input.mzid"/> + <output name="out" file="IDFileConverter_31_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="mz_name" value=""/> + <param name="peptideprophet_analyzed" value="false"/> + <param name="score_type" value="qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_IDFilter"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_1_input.idXML"/> + <output name="out" file="IDFilter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="proteins" value="IDFilter_1_input.fas"/> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_3_input.idXML"/> + <output name="out" file="IDFilter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="peptides" value="IDFilter_3_2_input.idXML"/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_4_input.idXML"/> + <output name="out" file="IDFilter_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.08"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_5_input.idXML"/> + <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="32.0"/> + <param name="prot" value="25.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_5_input.idXML"/> + <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="32.0"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_5_input.idXML"/> + <output name="out" file="IDFilter_5b_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="25.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_5_input.idXML"/> + <output name="out" file="IDFilter_5c_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="true"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="25.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_6_input.idXML"/> + <output name="out" file="IDFilter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="2"/> + <param name="n_protein_hits" value="10"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="true"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_7_input.idXML"/> + <output name="out" file="IDFilter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_8_input.idXML"/> + <output name="out" file="IDFilter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value="200:350"/> + <param name="mz" value="999:1000"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_9_input.idXML"/> + <output name="out" file="IDFilter_9_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.05"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_10_input.idXML"/> + <output name="out" file="IDFilter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="true"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="0.3"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_11_input.idXML"/> + <output name="out" file="IDFilter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="true"/> + <param name="delete_unreferenced_peptide_hits" value="true"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_12_input.idXML"/> + <output name="out" file="IDFilter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="fasta" value="IDFilter_12_input.fasta"/> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_13_input.idXML"/> + <output name="out" file="IDFilter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="fasta" value="IDFilter_13_input.fasta"/> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_14_input.idXML"/> + <output name="out" file="IDFilter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="fasta" value="IDFilter_14_input.fasta"/> + <param name="enzyme" value="Trypsin/P"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_15_input.idXML"/> + <output name="out" file="IDFilter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="fasta" value="IDFilter_15_input.fasta"/> + <param name="enzyme" value="Trypsin/P"/> + <param name="specificity" value="semi"/> + <param name="missed_cleavages" value="1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_16_input.idXML"/> + <output name="out" file="IDFilter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="fasta" value="IDFilter_16_input.fasta"/> + <param name="enzyme" value="Trypsin/P"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="1"/> + <param name="methionine_cleavage" value="true"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> + <output name="out" file="IDFilter_17_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":2"/> + <param name="enzyme" value="Lys-N"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> + <output name="out" file="IDFilter_18_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value="2:"/> + <param name="enzyme" value="Lys-N"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> + <output name="out" file="IDFilter_19_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value="1:3"/> + <param name="enzyme" value="Lys-N"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> + <output name="out" file="IDFilter_20_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value="1:0"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""calcMZ" "gt" "750.0""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_16_input.idXML"/> + <output name="out" file="IDFilter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""end" "ne" "23""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFilter_16_input.idXML"/> + <output name="out" file="IDFilter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDMapper_2_output.consensusXML"/> + <output name="out" file="IDFilter_23_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.0"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""Q9HP81""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="remove_duplicate_psm" value="false"/> + <param name="remove_peptide_hits_by_metavalue" value=""/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="Epifany_3_out.consensusXML"/> + <output name="out" file="IDFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="var_mods" value="false"/> + <param name="remove_shared_peptides" value="false"/> + <param name="keep_unreferenced_protein_hits" value="false"/> + <param name="remove_decoys" value="false"/> + <param name="delete_unreferenced_peptide_hits" value="false"/> + <section name="precursor"> + <param name="rt" value=":"/> + <param name="mz" value=":"/> + <param name="length" value=":"/> + <param name="charge" value=":"/> + </section> + <section name="score"> + <param name="pep" value="0.0"/> + <param name="prot" value="0.0"/> + <param name="protgroup" value="0.99"/> + </section> + <section name="whitelist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications" value=""/> + </section> + <section name="in_silico_digestion"> + <param name="enzyme" value="Trypsin"/> + <param name="specificity" value="full"/> + <param name="missed_cleavages" value="-1"/> + <param name="methionine_cleavage" value="false"/> + </section> + <section name="missed_cleavages"> + <param name="number_of_missed_cleavages" value=":"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="rt"> + <param name="p_value" value="0.0"/> + <param name="p_value_1st_dim" value="0.0"/> + </section> + <section name="mz"> + <param name="error" value="-1.0"/> + <param name="unit" value="ppm"/> + </section> + <section name="best"> + <param name="n_peptide_hits" value="0"/> + <param name="n_protein_hits" value="0"/> + <param name="strict" value="false"/> + <param name="n_to_m_peptide_hits" value=":"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_IDMapper"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_charge" value="true"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="id" value="IDMapper_1_input.idXML"/> + <param name="in" value="IDMapper_1_input.featureXML"/> + <output name="out" file="IDMapper_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="rt_tolerance" value="5.0"/> + <param name="mz_tolerance" value="1.0"/> + <param name="mz_measure" value="Da"/> + <param name="mz_reference" value="precursor"/> + <section name="feature"> + <param name="use_centroid_rt" value="false"/> + <param name="use_centroid_mz" value="false"/> + </section> + <section name="consensus"> + <param name="use_subelements" value="false"/> + <param name="annotate_ids_with_subelements" value="false"/> + </section> + <section name="spectra"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_charge" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="id" value="IDMapper_2_input.idXML"/> + <param name="in" value="IDMapper_2_input.consensusXML"/> + <output name="out" file="IDMapper_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="rt_tolerance" value="5.0"/> + <param name="mz_tolerance" value="1.0"/> + <param name="mz_measure" value="Da"/> + <param name="mz_reference" value="precursor"/> + <section name="feature"> + <param name="use_centroid_rt" value="false"/> + <param name="use_centroid_mz" value="true"/> + </section> + <section name="consensus"> + <param name="use_subelements" value="false"/> + <param name="annotate_ids_with_subelements" value="false"/> + </section> + <section name="spectra"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_charge" value="true"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="id" value="IDMapper_3_input.idXML"/> + <param name="in" value="IDMapper_3_input.featureXML"/> + <output name="out" file="IDMapper_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="rt_tolerance" value="4.0"/> + <param name="mz_tolerance" value="3.0"/> + <param name="mz_measure" value="ppm"/> + <param name="mz_reference" value="precursor"/> + <section name="feature"> + <param name="use_centroid_rt" value="false"/> + <param name="use_centroid_mz" value="true"/> + </section> + <section name="consensus"> + <param name="use_subelements" value="false"/> + <param name="annotate_ids_with_subelements" value="false"/> + </section> + <section name="spectra"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_charge" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="id" value="IDMapper_4_input.idXML"/> + <param name="in" value="IDMapper_4_input.featureXML"/> + <output name="out" file="IDMapper_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="rt_tolerance" value="10.0"/> + <param name="mz_tolerance" value="20.0"/> + <param name="mz_measure" value="ppm"/> + <param name="mz_reference" value="peptide"/> + <section name="feature"> + <param name="use_centroid_rt" value="false"/> + <param name="use_centroid_mz" value="true"/> + </section> + <section name="consensus"> + <param name="use_subelements" value="false"/> + <param name="annotate_ids_with_subelements" value="false"/> + </section> + <section name="spectra"> + <param name="_in" value="IDMapper_4_input.mzML"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="ignore_charge" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="id" value="IDMapper_5_input.idXML"/> + <param name="in" value="IDMapper_5_input.featureXML"/> + <output name="out" file="IDMapper_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="rt_tolerance" value="20.0"/> + <param name="mz_tolerance" value="10.0"/> + <param name="mz_measure" value="ppm"/> + <param name="mz_reference" value="peptide"/> + <section name="feature"> + <param name="use_centroid_rt" value="false"/> + <param name="use_centroid_mz" value="false"/> + </section> + <section name="consensus"> + <param name="use_subelements" value="false"/> + <param name="annotate_ids_with_subelements" value="false"/> + </section> + <section name="spectra"> + <param name="_in" value="IDMapper_5_input.mzML"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_IDMassAccuracy"> + <test expect_num_outputs="5"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="number_of_bins" value="10"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="spectra.mzML"/> + <param name="id_in" value="MSGFPlusAdapter_1_out.idXML"/> + <output name="out_precursor" file="IDMassAccuracy_1_out_precursor.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="precursor_error_ppm" value="false"/> + <output name="out_fragment" file="IDMassAccuracy_1_out_fragment.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="fragment_error_ppm" value="false"/> + <param name="fragment_mass_tolerance" value="0.5"/> + <output name="out_precursor_fit" file="IDMassAccuracy_1_out_precursor_fit.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <output name="out_fragment_fit" file="IDMassAccuracy_1_out_fragment_fit.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_precursor_FLAG,out_fragment_FLAG,out_precursor_fit_FLAG,out_fragment_fit_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_IDMerger"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input2.idXML"/> + <output name="out" file="IDMerger_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="annotate_file_origin" value="true"/> + <param name="pepxml_protxml" value="false"/> + <param name="merge_proteins_add_PSMs" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDMerger_2_input1.idXML,IDMerger_2_input2.idXML"/> + <output name="out" file="IDMerger_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="annotate_file_origin" value="false"/> + <param name="pepxml_protxml" value="true"/> + <param name="merge_proteins_add_PSMs" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input1_2.idXML"/> + <output name="out" file="IDMerger_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="annotate_file_origin" value="false"/> + <param name="pepxml_protxml" value="false"/> + <param name="merge_proteins_add_PSMs" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="degenerated_empty.idXML,degenerated_empty_2.idXML"/> + <output name="out" file="IDMerger_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="annotate_file_origin" value="false"/> + <param name="pepxml_protxml" value="false"/> + <param name="merge_proteins_add_PSMs" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDMerger_2_input1.idXML"/> + <output name="out" file="IDMerger_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="add_to" value="IDMerger_5_input1.idXML"/> + <param name="annotate_file_origin" value="false"/> + <param name="pepxml_protxml" value="false"/> + <param name="merge_proteins_add_PSMs" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDRipper_3_input1.idXML,IDRipper_3_input2.idXML"/> + <output name="out" file="IDRipper_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="annotate_file_origin" value="true"/> + <param name="pepxml_protxml" value="false"/> + <param name="merge_proteins_add_PSMs" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_IDPosteriorErrorProbability"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="fdr_for_targets_smaller" value="0.05"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDPosteriorErrorProbability_Mascot_input.idXML"/> + <output name="out" file="IDPosteriorErrorProbability_Mascot_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="split_charge" value="false"/> + <param name="top_hits_only" value="false"/> + <param name="ignore_bad_data" value="false"/> + <param name="prob_correct" value="false"/> + <section name="fit_algorithm"> + <param name="number_of_bins" value="100"/> + <param name="incorrectly_assigned" value="Gumbel"/> + <param name="max_nr_iterations" value="1000"/> + <param name="neg_log_delta" value="6"/> + <param name="outlier_handling" value="ignore_iqr_outliers"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="fdr_for_targets_smaller" value="0.05"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDPosteriorErrorProbability_XTandem_input.idXML"/> + <output name="out" file="IDPosteriorErrorProbability_XTandem_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="split_charge" value="false"/> + <param name="top_hits_only" value="false"/> + <param name="ignore_bad_data" value="false"/> + <param name="prob_correct" value="false"/> + <section name="fit_algorithm"> + <param name="number_of_bins" value="100"/> + <param name="incorrectly_assigned" value="Gumbel"/> + <param name="max_nr_iterations" value="1000"/> + <param name="neg_log_delta" value="6"/> + <param name="outlier_handling" value="ignore_iqr_outliers"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="fdr_for_targets_smaller" value="0.05"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/> + <output name="out" file="IDPosteriorErrorProbability_OMSSA_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="split_charge" value="false"/> + <param name="top_hits_only" value="false"/> + <param name="ignore_bad_data" value="false"/> + <param name="prob_correct" value="false"/> + <section name="fit_algorithm"> + <param name="number_of_bins" value="100"/> + <param name="incorrectly_assigned" value="Gumbel"/> + <param name="max_nr_iterations" value="1000"/> + <param name="neg_log_delta" value="6"/> + <param name="outlier_handling" value="ignore_iqr_outliers"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="fdr_for_targets_smaller" value="0.05"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDPosteriorErrorProbability_OMSSA_input2.idXML"/> + <output name="out" file="IDPosteriorErrorProbability_OMSSA_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="split_charge" value="true"/> + <param name="top_hits_only" value="false"/> + <param name="ignore_bad_data" value="false"/> + <param name="prob_correct" value="false"/> + <section name="fit_algorithm"> + <param name="number_of_bins" value="100"/> + <param name="incorrectly_assigned" value="Gumbel"/> + <param name="max_nr_iterations" value="1000"/> + <param name="neg_log_delta" value="6"/> + <param name="outlier_handling" value="ignore_iqr_outliers"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="fdr_for_targets_smaller" value="0.05"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDPosteriorErrorProbability_XTandem_input2.idXML"/> + <output name="out" file="IDPosteriorErrorProbability_XTandem_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="split_charge" value="true"/> + <param name="top_hits_only" value="false"/> + <param name="ignore_bad_data" value="false"/> + <param name="prob_correct" value="false"/> + <section name="fit_algorithm"> + <param name="number_of_bins" value="100"/> + <param name="incorrectly_assigned" value="Gumbel"/> + <param name="max_nr_iterations" value="1000"/> + <param name="neg_log_delta" value="6"/> + <param name="outlier_handling" value="ignore_iqr_outliers"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="fdr_for_targets_smaller" value="0.05"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDPosteriorErrorProbability_Mascot_input2.idXML"/> + <output name="out" file="IDPosteriorErrorProbability_Mascot_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="split_charge" value="true"/> + <param name="top_hits_only" value="false"/> + <param name="ignore_bad_data" value="false"/> + <param name="prob_correct" value="false"/> + <section name="fit_algorithm"> + <param name="number_of_bins" value="100"/> + <param name="incorrectly_assigned" value="Gumbel"/> + <param name="max_nr_iterations" value="1000"/> + <param name="neg_log_delta" value="6"/> + <param name="outlier_handling" value="ignore_iqr_outliers"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="fdr_for_targets_smaller" value="0.05"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDPosteriorErrorProbability_bad_data.idXML"/> + <output name="out" file="IDPosteriorErrorProbability_bad_data_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="split_charge" value="false"/> + <param name="top_hits_only" value="false"/> + <param name="ignore_bad_data" value="true"/> + <param name="prob_correct" value="false"/> + <section name="fit_algorithm"> + <param name="number_of_bins" value="100"/> + <param name="incorrectly_assigned" value="Gumbel"/> + <param name="max_nr_iterations" value="1000"/> + <param name="neg_log_delta" value="6"/> + <param name="outlier_handling" value="ignore_iqr_outliers"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="fdr_for_targets_smaller" value="0.05"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/> + <output name="out" file="IDPosteriorErrorProbability_prob_correct_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="split_charge" value="false"/> + <param name="top_hits_only" value="false"/> + <param name="ignore_bad_data" value="false"/> + <param name="prob_correct" value="true"/> + <section name="fit_algorithm"> + <param name="number_of_bins" value="100"/> + <param name="incorrectly_assigned" value="Gumbel"/> + <param name="max_nr_iterations" value="1000"/> + <param name="neg_log_delta" value="6"/> + <param name="outlier_handling" value="ignore_iqr_outliers"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_IDRipper"/> + <xml name="autotest_IDRTCalibration"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDRTCalibration_1_input.idXML"/> + <output name="out" file="IDRTCalibration_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="calibrant_1_reference" value="0.1"/> + <param name="calibrant_2_reference" value="0.9"/> + <param name="calibrant_1_input" value="10.0"/> + <param name="calibrant_2_input" value="90.0"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="degenerated_empty.idXML"/> + <output name="out" file="IDRTCalibration_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="calibrant_1_reference" value="0.1"/> + <param name="calibrant_2_reference" value="0.9"/> + <param name="calibrant_1_input" value="10.0"/> + <param name="calibrant_2_input" value="90.0"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_IDScoreSwitcher"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDFileConverter_12_output.idXML"/> + <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="proteins" value="false"/> + <param name="new_score" value="Percolator_PEP"/> + <param name="new_score_orientation" value="lower_better"/> + <param name="new_score_type" value="Posterior Error Probability"/> + <param name="old_score" value="Percolator_qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDScoreSwitcher_2_input.idXML"/> + <output name="out" file="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="proteins" value="true"/> + <param name="new_score" value="Posterior Probability_score"/> + <param name="new_score_orientation" value="higher_better"/> + <param name="new_score_type" value="Posterior Probability"/> + <param name="old_score" value=""/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_IDSplitter"> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDMapper_1_output.featureXML"/> + <output name="out" file="IDSplitter_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="id_out" file="IDSplitter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,id_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_InternalCalibration"> + <test expect_num_outputs="4"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="InternalCalibration_1_BSA1.mzML"/> + <output name="out" file="InternalCalibration_1_BSA1_out.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="ppm_match_tolerance" value="25.0"/> + <param name="ms_level" value="1"/> + <param name="RT_chunking" value="-1.0"/> + <section name="cal"> + <param name="id_in" value="InternalCalibration_1_BSA1_OMSSA.idXML"/> + <param name="lock_require_mono" value="false"/> + <param name="lock_require_iso" value="false"/> + <param name="model_type" value="linear"/> + </section> + <section name="RANSAC"> + <param name="enabled" value="true"/> + <param name="threshold" value="1.0"/> + <param name="pc_inliers" value="30"/> + <param name="iter" value="500"/> + </section> + <section name="goodness"> + <param name="median" value="4.0"/> + <param name="MAD" value="2.0"/> + </section> + <section name="quality_control"/> + <output name="quality_control_models" file="InternalCalibration_1_models.csv" compare="sim_size" delta="5700" ftype="csv"/> + <output name="quality_control_residuals" file="InternalCalibration_1_residuals.csv" compare="sim_size" delta="5700" ftype="csv"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="4"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="InternalCalibration_2_lockmass.mzML.gz"/> + <output name="out" file="InternalCalibration_2_lockmass.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="ppm_match_tolerance" value="25.0"/> + <param name="ms_level" value="1 2 3"/> + <param name="RT_chunking" value="60.0"/> + <section name="cal"> + <param name="lock_in" value="InternalCalibration_2_lock.csv" ftype="csv"/> + <param name="lock_require_mono" value="true"/> + <param name="lock_require_iso" value="false"/> + <param name="model_type" value="linear"/> + </section> + <section name="RANSAC"> + <param name="enabled" value="false"/> + <param name="threshold" value="10.0"/> + <param name="pc_inliers" value="30"/> + <param name="iter" value="70"/> + </section> + <section name="goodness"> + <param name="median" value="4.0"/> + <param name="MAD" value="2.0"/> + </section> + <section name="quality_control"/> + <output name="quality_control_models" file="InternalCalibration_2_models.csv" compare="sim_size" delta="5700" ftype="csv"/> + <output name="quality_control_residuals" file="InternalCalibration_2_residuals.csv" compare="sim_size" delta="5700" ftype="csv"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_IsobaricAnalyzer"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="type" value="itraq4plex"/> + <param name="in" value="IsobaricAnalyzer_input_1.mzML"/> + <output name="out" file="IsobaricAnalyzer_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="extraction"> + <param name="select_activation" value=""/> + <param name="reporter_mass_shift" value="0.1"/> + <param name="min_precursor_intensity" value="1.0"/> + <param name="keep_unannotated_precursor" value="true"/> + <param name="min_reporter_intensity" value="0.0"/> + <param name="discard_low_intensity_quantifications" value="false"/> + <param name="min_precursor_purity" value="0.0"/> + <param name="precursor_isotope_deviation" value="10.0"/> + <param name="purity_interpolation" value="true"/> + </section> + <section name="itraq4plex"> + <param name="channel_114_description" value="l1"/> + <param name="channel_115_description" value="l2"/> + <param name="channel_116_description" value="l3"/> + <param name="channel_117_description" value="lung"/> + <param name="reference_channel" value="114"/> + <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> + </section> + <section name="itraq8plex"> + <param name="channel_113_description" value=""/> + <param name="channel_114_description" value=""/> + <param name="channel_115_description" value=""/> + <param name="channel_116_description" value=""/> + <param name="channel_117_description" value=""/> + <param name="channel_118_description" value=""/> + <param name="channel_119_description" value=""/> + <param name="channel_121_description" value=""/> + <param name="reference_channel" value="113"/> + <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> + </section> + <section name="quantification"> + <param name="isotope_correction" value="true"/> + <param name="normalization" value="false"/> + </section> + <section name="tmt10plex"> + <param name="channel_126_description" value=""/> + <param name="channel_127N_description" value=""/> + <param name="channel_127C_description" value=""/> + <param name="channel_128N_description" value=""/> + <param name="channel_128C_description" value=""/> + <param name="channel_129N_description" value=""/> + <param name="channel_129C_description" value=""/> + <param name="channel_130N_description" value=""/> + <param name="channel_130C_description" value=""/> + <param name="channel_131_description" value=""/> + <param name="reference_channel" value="126"/> + <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> + </section> + <section name="tmt11plex"> + <param name="channel_126_description" value=""/> + <param name="channel_127N_description" value=""/> + <param name="channel_127C_description" value=""/> + <param name="channel_128N_description" value=""/> + <param name="channel_128C_description" value=""/> + <param name="channel_129N_description" value=""/> + <param name="channel_129C_description" value=""/> + <param name="channel_130N_description" value=""/> + <param name="channel_130C_description" value=""/> + <param name="channel_131N_description" value=""/> + <param name="channel_131C_description" value=""/> + <param name="reference_channel" value="126"/> + <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> + </section> + <section name="tmt16plex"> + <param name="channel_126_description" value=""/> + <param name="channel_127N_description" value=""/> + <param name="channel_127C_description" value=""/> + <param name="channel_128N_description" value=""/> + <param name="channel_128C_description" value=""/> + <param name="channel_129N_description" value=""/> + <param name="channel_129C_description" value=""/> + <param name="channel_130N_description" value=""/> + <param name="channel_130C_description" value=""/> + <param name="channel_131N_description" value=""/> + <param name="channel_131C_description" value=""/> + <param name="channel_132N_description" value=""/> + <param name="channel_132C_description" value=""/> + <param name="channel_133N_description" value=""/> + <param name="channel_133C_description" value=""/> + <param name="channel_134N_description" value=""/> + <param name="reference_channel" value="126"/> + <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> + </section> + <section name="tmt6plex"> + <param name="channel_126_description" value=""/> + <param name="channel_127_description" value=""/> + <param name="channel_128_description" value=""/> + <param name="channel_129_description" value=""/> + <param name="channel_130_description" value=""/> + <param name="channel_131_description" value=""/> + <param name="reference_channel" value="126"/> + <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="type" value="itraq4plex"/> + <param name="in" value="TMTTenPlexMethod_test.mzML"/> + <output name="out" file="TMTTenPlexMethod_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="extraction"> + <param name="select_activation" value="High-energy collision-induced dissociation"/> + <param name="reporter_mass_shift" value="0.002"/> + <param name="min_precursor_intensity" value="1.0"/> + <param name="keep_unannotated_precursor" value="true"/> + <param name="min_reporter_intensity" value="0.0"/> + <param name="discard_low_intensity_quantifications" value="false"/> + <param name="min_precursor_purity" value="0.0"/> + <param name="precursor_isotope_deviation" value="10.0"/> + <param name="purity_interpolation" value="true"/> + </section> + <section name="itraq4plex"> + <param name="channel_114_description" value=""/> + <param name="channel_115_description" value=""/> + <param name="channel_116_description" value=""/> + <param name="channel_117_description" value=""/> + <param name="reference_channel" value="114"/> + <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> + </section> + <section name="itraq8plex"> + <param name="channel_113_description" value=""/> + <param name="channel_114_description" value=""/> + <param name="channel_115_description" value=""/> + <param name="channel_116_description" value=""/> + <param name="channel_117_description" value=""/> + <param name="channel_118_description" value=""/> + <param name="channel_119_description" value=""/> + <param name="channel_121_description" value=""/> + <param name="reference_channel" value="113"/> + <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> + </section> + <section name="quantification"> + <param name="isotope_correction" value="true"/> + <param name="normalization" value="false"/> + </section> + <section name="tmt10plex"> + <param name="channel_126_description" value=""/> + <param name="channel_127N_description" value=""/> + <param name="channel_127C_description" value=""/> + <param name="channel_128N_description" value=""/> + <param name="channel_128C_description" value=""/> + <param name="channel_129N_description" value=""/> + <param name="channel_129C_description" value=""/> + <param name="channel_130N_description" value=""/> + <param name="channel_130C_description" value=""/> + <param name="channel_131_description" value=""/> + <param name="reference_channel" value="126"/> + <param name="correction_matrix" value=""0.0/0.0/5.0/0.0" "0.0/0.2/4.6/0.0" "0.0/0.2/4.6/0.3" "0.0/0.9/4.7/0.2" "0.0/0.5/3.2/0.0" "0.0/0.7/3.3/0.0" "0.0/1.3/2.5/0.0" "0.0/1.2/2.8/2.7" "0.0/1.5/2.0/0.0" "0.0/1.5/1.9/0.0""/> + </section> + <section name="tmt11plex"> + <param name="channel_126_description" value=""/> + <param name="channel_127N_description" value=""/> + <param name="channel_127C_description" value=""/> + <param name="channel_128N_description" value=""/> + <param name="channel_128C_description" value=""/> + <param name="channel_129N_description" value=""/> + <param name="channel_129C_description" value=""/> + <param name="channel_130N_description" value=""/> + <param name="channel_130C_description" value=""/> + <param name="channel_131N_description" value=""/> + <param name="channel_131C_description" value=""/> + <param name="reference_channel" value="126"/> + <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> + </section> + <section name="tmt16plex"> + <param name="channel_126_description" value=""/> + <param name="channel_127N_description" value=""/> + <param name="channel_127C_description" value=""/> + <param name="channel_128N_description" value=""/> + <param name="channel_128C_description" value=""/> + <param name="channel_129N_description" value=""/> + <param name="channel_129C_description" value=""/> + <param name="channel_130N_description" value=""/> + <param name="channel_130C_description" value=""/> + <param name="channel_131N_description" value=""/> + <param name="channel_131C_description" value=""/> + <param name="channel_132N_description" value=""/> + <param name="channel_132C_description" value=""/> + <param name="channel_133N_description" value=""/> + <param name="channel_133C_description" value=""/> + <param name="channel_134N_description" value=""/> + <param name="reference_channel" value="126"/> + <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> + </section> + <section name="tmt6plex"> + <param name="channel_126_description" value=""/> + <param name="channel_127_description" value=""/> + <param name="channel_128_description" value=""/> + <param name="channel_129_description" value=""/> + <param name="channel_130_description" value=""/> + <param name="channel_131_description" value=""/> + <param name="reference_channel" value="126"/> + <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="type" value="itraq4plex"/> + <param name="in" value="TMTTenPlexMethod_test.mzML"/> + <output name="out" file="TMTElevenPlexMethod_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="extraction"> + <param name="select_activation" value="High-energy collision-induced dissociation"/> + <param name="reporter_mass_shift" value="0.002"/> + <param name="min_precursor_intensity" value="1.0"/> + <param name="keep_unannotated_precursor" value="true"/> + <param name="min_reporter_intensity" value="0.0"/> + <param name="discard_low_intensity_quantifications" value="false"/> + <param name="min_precursor_purity" value="0.0"/> + <param name="precursor_isotope_deviation" value="10.0"/> + <param name="purity_interpolation" value="true"/> + </section> + <section name="itraq4plex"> + <param name="channel_114_description" value=""/> + <param name="channel_115_description" value=""/> + <param name="channel_116_description" value=""/> + <param name="channel_117_description" value=""/> + <param name="reference_channel" value="114"/> + <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> + </section> + <section name="itraq8plex"> + <param name="channel_113_description" value=""/> + <param name="channel_114_description" value=""/> + <param name="channel_115_description" value=""/> + <param name="channel_116_description" value=""/> + <param name="channel_117_description" value=""/> + <param name="channel_118_description" value=""/> + <param name="channel_119_description" value=""/> + <param name="channel_121_description" value=""/> + <param name="reference_channel" value="113"/> + <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> + </section> + <section name="quantification"> + <param name="isotope_correction" value="true"/> + <param name="normalization" value="false"/> + </section> + <section name="tmt10plex"> + <param name="channel_126_description" value=""/> + <param name="channel_127N_description" value=""/> + <param name="channel_127C_description" value=""/> + <param name="channel_128N_description" value=""/> + <param name="channel_128C_description" value=""/> + <param name="channel_129N_description" value=""/> + <param name="channel_129C_description" value=""/> + <param name="channel_130N_description" value=""/> + <param name="channel_130C_description" value=""/> + <param name="channel_131_description" value=""/> + <param name="reference_channel" value="126"/> + <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> + </section> + <section name="tmt11plex"> + <param name="channel_126_description" value=""/> + <param name="channel_127N_description" value=""/> + <param name="channel_127C_description" value=""/> + <param name="channel_128N_description" value=""/> + <param name="channel_128C_description" value=""/> + <param name="channel_129N_description" value=""/> + <param name="channel_129C_description" value=""/> + <param name="channel_130N_description" value=""/> + <param name="channel_130C_description" value=""/> + <param name="channel_131N_description" value=""/> + <param name="channel_131C_description" value=""/> + <param name="reference_channel" value="126"/> + <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> + </section> + <section name="tmt16plex"> + <param name="channel_126_description" value=""/> + <param name="channel_127N_description" value=""/> + <param name="channel_127C_description" value=""/> + <param name="channel_128N_description" value=""/> + <param name="channel_128C_description" value=""/> + <param name="channel_129N_description" value=""/> + <param name="channel_129C_description" value=""/> + <param name="channel_130N_description" value=""/> + <param name="channel_130C_description" value=""/> + <param name="channel_131N_description" value=""/> + <param name="channel_131C_description" value=""/> + <param name="channel_132N_description" value=""/> + <param name="channel_132C_description" value=""/> + <param name="channel_133N_description" value=""/> + <param name="channel_133C_description" value=""/> + <param name="channel_134N_description" value=""/> + <param name="reference_channel" value="126"/> + <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> + </section> + <section name="tmt6plex"> + <param name="channel_126_description" value=""/> + <param name="channel_127_description" value=""/> + <param name="channel_128_description" value=""/> + <param name="channel_129_description" value=""/> + <param name="channel_130_description" value=""/> + <param name="channel_131_description" value=""/> + <param name="reference_channel" value="126"/> + <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="type" value="tmt10plex"/> + <param name="in" value="MS3_nonHierarchical.mzML"/> + <output name="out" file="MS3TMT10Plex_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="extraction"> + <param name="select_activation" value="Collision-induced dissociation"/> + <param name="reporter_mass_shift" value="0.002"/> + <param name="min_precursor_intensity" value="1.0"/> + <param name="keep_unannotated_precursor" value="true"/> + <param name="min_reporter_intensity" value="0.0"/> + <param name="discard_low_intensity_quantifications" value="false"/> + <param name="min_precursor_purity" value="0.0"/> + <param name="precursor_isotope_deviation" value="10.0"/> + <param name="purity_interpolation" value="true"/> + </section> + <section name="itraq4plex"> + <param name="channel_114_description" value=""/> + <param name="channel_115_description" value=""/> + <param name="channel_116_description" value=""/> + <param name="channel_117_description" value=""/> + <param name="reference_channel" value="114"/> + <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> + </section> + <section name="itraq8plex"> + <param name="channel_113_description" value=""/> + <param name="channel_114_description" value=""/> + <param name="channel_115_description" value=""/> + <param name="channel_116_description" value=""/> + <param name="channel_117_description" value=""/> + <param name="channel_118_description" value=""/> + <param name="channel_119_description" value=""/> + <param name="channel_121_description" value=""/> + <param name="reference_channel" value="113"/> + <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> + </section> + <section name="quantification"> + <param name="isotope_correction" value="true"/> + <param name="normalization" value="false"/> + </section> + <section name="tmt10plex"> + <param name="channel_126_description" value=""/> + <param name="channel_127N_description" value=""/> + <param name="channel_127C_description" value=""/> + <param name="channel_128N_description" value=""/> + <param name="channel_128C_description" value=""/> + <param name="channel_129N_description" value=""/> + <param name="channel_129C_description" value=""/> + <param name="channel_130N_description" value=""/> + <param name="channel_130C_description" value=""/> + <param name="channel_131_description" value=""/> + <param name="reference_channel" value="126"/> + <param name="correction_matrix" value=""0.0/0.0/5.09/0.0" "0.0/0.25/5.27/0.0" "0.0/0.37/5.36/0.15" "0.0/0.65/4.17/0.1" "0.08/0.49/3.06/0.0" "0.01/0.71/3.07/0.0" "0.0/1.32/2.62/0.0" "0.02/1.28/2.75/2.53" "0.03/2.08/2.23/0.0" "0.08/1.99/1.65/0.0""/> + </section> + <section name="tmt11plex"> + <param name="channel_126_description" value=""/> + <param name="channel_127N_description" value=""/> + <param name="channel_127C_description" value=""/> + <param name="channel_128N_description" value=""/> + <param name="channel_128C_description" value=""/> + <param name="channel_129N_description" value=""/> + <param name="channel_129C_description" value=""/> + <param name="channel_130N_description" value=""/> + <param name="channel_130C_description" value=""/> + <param name="channel_131N_description" value=""/> + <param name="channel_131C_description" value=""/> + <param name="reference_channel" value="126"/> + <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> + </section> + <section name="tmt16plex"> + <param name="channel_126_description" value=""/> + <param name="channel_127N_description" value=""/> + <param name="channel_127C_description" value=""/> + <param name="channel_128N_description" value=""/> + <param name="channel_128C_description" value=""/> + <param name="channel_129N_description" value=""/> + <param name="channel_129C_description" value=""/> + <param name="channel_130N_description" value=""/> + <param name="channel_130C_description" value=""/> + <param name="channel_131N_description" value=""/> + <param name="channel_131C_description" value=""/> + <param name="channel_132N_description" value=""/> + <param name="channel_132C_description" value=""/> + <param name="channel_133N_description" value=""/> + <param name="channel_133C_description" value=""/> + <param name="channel_134N_description" value=""/> + <param name="reference_channel" value="126"/> + <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> + </section> + <section name="tmt6plex"> + <param name="channel_126_description" value=""/> + <param name="channel_127_description" value=""/> + <param name="channel_128_description" value=""/> + <param name="channel_129_description" value=""/> + <param name="channel_130_description" value=""/> + <param name="channel_131_description" value=""/> + <param name="reference_channel" value="126"/> + <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_LabeledEval"> +</xml> + <xml name="autotest_LuciphorAdapter"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="LuciphorAdapter_1_input.mzML"/> + <param name="id" value="LuciphorAdapter_1_input.idXML"/> + <output name="out" file="LuciphorAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="fragment_method" value="CID"/> + <param name="fragment_mass_tolerance" value="0.5"/> + <param name="fragment_error_units" value="Da"/> + <param name="min_mz" value="150.0"/> + <param name="target_modifications" value="Phospho (S),Phospho (T),Phospho (Y)"/> + <param name="neutral_losses" value=""sty -H3PO4 -97.97690""/> + <param name="decoy_mass" value="79.966331"/> + <param name="decoy_neutral_losses" value=""X -H3PO4 -97.97690""/> + <param name="max_charge_state" value="5"/> + <param name="max_peptide_length" value="40"/> + <param name="max_num_perm" value="16384"/> + <param name="modeling_score_threshold" value="0.95"/> + <param name="scoring_threshold" value="0.0"/> + <param name="min_num_psms_model" value="1"/> + <param name="run_mode" value="0"/> + <param name="rt_tolerance" value="0.01"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_MapAlignerIdentification"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/> + <output_collection name="out" count="2"/> + <section name="reference"> + <param name="index" value="0"/> + </section> + <section name="algorithm"> + <param name="score_cutoff" value="false"/> + <param name="min_score" value="0.05"/> + <param name="min_run_occur" value="2"/> + <param name="max_rt_shift" value="0.0"/> + <param name="use_unassigned_peptides" value="true"/> + <param name="use_feature_rt" value="false"/> + </section> + <section name="model"> + <param name="type" value="b_spline"/> + <section name="linear"> + <param name="symmetric_regression" value="false"/> + <param name="x_weight" value=""/> + <param name="y_weight" value=""/> + <param name="x_datum_min" value="1e-15"/> + <param name="x_datum_max" value="1000000000000000.0"/> + <param name="y_datum_min" value="1e-15"/> + <param name="y_datum_max" value="1000000000000000.0"/> + </section> + <section name="b_spline"> + <param name="wavelength" value="0.0"/> + <param name="num_nodes" value="5"/> + <param name="extrapolate" value="linear"/> + <param name="boundary_condition" value="2"/> + </section> + <section name="lowess"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + <section name="interpolated"> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="two-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapAlignerIdentification_1_input1.featureXML"/> + <output_collection name="out" count="1"/> + <section name="reference"> + <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/> + <param name="index" value="0"/> + </section> + <section name="algorithm"> + <param name="score_cutoff" value="false"/> + <param name="min_score" value="0.05"/> + <param name="min_run_occur" value="2"/> + <param name="max_rt_shift" value="0.0"/> + <param name="use_unassigned_peptides" value="true"/> + <param name="use_feature_rt" value="false"/> + </section> + <section name="model"> + <param name="type" value="b_spline"/> + <section name="linear"> + <param name="symmetric_regression" value="false"/> + <param name="x_weight" value=""/> + <param name="y_weight" value=""/> + <param name="x_datum_min" value="1e-15"/> + <param name="x_datum_max" value="1000000000000000.0"/> + <param name="y_datum_min" value="1e-15"/> + <param name="y_datum_max" value="1000000000000000.0"/> + </section> + <section name="b_spline"> + <param name="wavelength" value="0.0"/> + <param name="num_nodes" value="5"/> + <param name="extrapolate" value="linear"/> + <param name="boundary_condition" value="2"/> + </section> + <section name="lowess"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + <section name="interpolated"> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="two-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapAlignerIdentification_1_input2.featureXML,MapAlignerIdentification_1_input1.featureXML"/> + <output_collection name="out" count="2"/> + <section name="reference"> + <param name="index" value="1"/> + </section> + <section name="algorithm"> + <param name="score_cutoff" value="false"/> + <param name="min_score" value="0.05"/> + <param name="min_run_occur" value="2"/> + <param name="max_rt_shift" value="0.0"/> + <param name="use_unassigned_peptides" value="true"/> + <param name="use_feature_rt" value="false"/> + </section> + <section name="model"> + <param name="type" value="b_spline"/> + <section name="linear"> + <param name="symmetric_regression" value="false"/> + <param name="x_weight" value=""/> + <param name="y_weight" value=""/> + <param name="x_datum_min" value="1e-15"/> + <param name="x_datum_max" value="1000000000000000.0"/> + <param name="y_datum_min" value="1e-15"/> + <param name="y_datum_max" value="1000000000000000.0"/> + </section> + <section name="b_spline"> + <param name="wavelength" value="0.0"/> + <param name="num_nodes" value="5"/> + <param name="extrapolate" value="linear"/> + <param name="boundary_condition" value="2"/> + </section> + <section name="lowess"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + <section name="interpolated"> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="two-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/> + <output_collection name="out" count="2"/> + <section name="reference"> + <param name="index" value="2"/> + </section> + <section name="algorithm"> + <param name="score_cutoff" value="false"/> + <param name="min_score" value="0.05"/> + <param name="min_run_occur" value="2"/> + <param name="max_rt_shift" value="0.0"/> + <param name="use_unassigned_peptides" value="true"/> + <param name="use_feature_rt" value="false"/> + </section> + <section name="model"> + <param name="type" value="b_spline"/> + <section name="linear"> + <param name="symmetric_regression" value="false"/> + <param name="x_weight" value=""/> + <param name="y_weight" value=""/> + <param name="x_datum_min" value="1e-15"/> + <param name="x_datum_max" value="1000000000000000.0"/> + <param name="y_datum_min" value="1e-15"/> + <param name="y_datum_max" value="1000000000000000.0"/> + </section> + <section name="b_spline"> + <param name="wavelength" value="0.0"/> + <param name="num_nodes" value="5"/> + <param name="extrapolate" value="linear"/> + <param name="boundary_condition" value="2"/> + </section> + <section name="lowess"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + <section name="interpolated"> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="two-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapAlignerIdentification_5_input1.consensusXML,MapAlignerIdentification_5_input2.consensusXML"/> + <output_collection name="out" count="2"/> + <section name="reference"> + <param name="index" value="0"/> + </section> + <section name="algorithm"> + <param name="score_cutoff" value="false"/> + <param name="min_score" value="0.05"/> + <param name="min_run_occur" value="2"/> + <param name="max_rt_shift" value="0.0"/> + <param name="use_unassigned_peptides" value="true"/> + <param name="use_feature_rt" value="false"/> + </section> + <section name="model"> + <param name="type" value="b_spline"/> + <section name="linear"> + <param name="symmetric_regression" value="false"/> + <param name="x_weight" value=""/> + <param name="y_weight" value=""/> + <param name="x_datum_min" value="1e-15"/> + <param name="x_datum_max" value="1000000000000000.0"/> + <param name="y_datum_min" value="1e-15"/> + <param name="y_datum_max" value="1000000000000000.0"/> + </section> + <section name="b_spline"> + <param name="wavelength" value="0.0"/> + <param name="num_nodes" value="5"/> + <param name="extrapolate" value="linear"/> + <param name="boundary_condition" value="2"/> + </section> + <section name="lowess"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + <section name="interpolated"> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="two-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapAlignerIdentification_1_input1.featureXML"/> + <output_collection name="trafo_out" count="1"/> + <section name="reference"> + <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/> + <param name="index" value="0"/> + </section> + <section name="algorithm"> + <param name="score_cutoff" value="false"/> + <param name="min_score" value="0.05"/> + <param name="min_run_occur" value="2"/> + <param name="max_rt_shift" value="0.0"/> + <param name="use_unassigned_peptides" value="true"/> + <param name="use_feature_rt" value="false"/> + </section> + <section name="model"> + <param name="type" value="b_spline"/> + <section name="linear"> + <param name="symmetric_regression" value="false"/> + <param name="x_weight" value=""/> + <param name="y_weight" value=""/> + <param name="x_datum_min" value="1e-15"/> + <param name="x_datum_max" value="1000000000000000.0"/> + <param name="y_datum_min" value="1e-15"/> + <param name="y_datum_max" value="1000000000000000.0"/> + </section> + <section name="b_spline"> + <param name="wavelength" value="0.0"/> + <param name="num_nodes" value="5"/> + <param name="extrapolate" value="linear"/> + <param name="boundary_condition" value="2"/> + </section> + <section name="lowess"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + <section name="interpolated"> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="two-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="true"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapAlignerIdentification_7_input1.idXML"/> + <output_collection name="out" count="1"/> + <output_collection name="trafo_out" count="1"/> + <section name="reference"> + <param name="file" value="MapAlignerIdentification_7_input2.idXML"/> + <param name="index" value="0"/> + </section> + <section name="algorithm"> + <param name="score_cutoff" value="false"/> + <param name="min_score" value="0.05"/> + <param name="min_run_occur" value="2"/> + <param name="max_rt_shift" value="0.5"/> + <param name="use_unassigned_peptides" value="true"/> + <param name="use_feature_rt" value="false"/> + </section> + <section name="model"> + <param name="type" value="b_spline"/> + <section name="linear"> + <param name="symmetric_regression" value="false"/> + <param name="x_weight" value=""/> + <param name="y_weight" value=""/> + <param name="x_datum_min" value="1e-15"/> + <param name="x_datum_max" value="1000000000000000.0"/> + <param name="y_datum_min" value="1e-15"/> + <param name="y_datum_max" value="1000000000000000.0"/> + </section> + <section name="b_spline"> + <param name="wavelength" value="0.0"/> + <param name="num_nodes" value="5"/> + <param name="extrapolate" value="linear"/> + <param name="boundary_condition" value="2"/> + </section> + <section name="lowess"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + <section name="interpolated"> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="two-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_MapAlignerPoseClustering"> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/> + <output_collection name="out" count="3"/> + <output_collection name="trafo_out" count="3"/> + <section name="reference"> + <param name="index" value="0"/> + </section> + <section name="algorithm"> + <param name="max_num_peaks_considered" value="400"/> + <section name="superimposer"> + <param name="mz_pair_max_distance" value="0.5"/> + <param name="rt_pair_distance_fraction" value="0.1"/> + <param name="num_used_points" value="2000"/> + <param name="scaling_bucket_size" value="0.005"/> + <param name="shift_bucket_size" value="3.0"/> + <param name="max_shift" value="1000.0"/> + <param name="max_scaling" value="2.0"/> + <param name="dump_buckets" value=""/> + <param name="dump_pairs" value=""/> + </section> + <section name="pairfinder"> + <param name="second_nearest_gap" value="2.0"/> + <param name="use_identifications" value="false"/> + <param name="ignore_charge" value="true"/> + <param name="ignore_adduct" value="true"/> + <section name="distance_RT"> + <param name="max_difference" value="30.0"/> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_MZ"> + <param name="max_difference" value="0.3"/> + <param name="unit" value="Da"/> + <param name="exponent" value="2.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_intensity"> + <param name="exponent" value="1.0"/> + <param name="weight" value="0.0"/> + <param name="log_transform" value="disabled"/> + </section> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapAlignerPoseClustering_2_input1.mzML,MapAlignerPoseClustering_2_input2.mzML,MapAlignerPoseClustering_2_input3.mzML"/> + <output_collection name="out" count="3"/> + <section name="reference"> + <param name="index" value="0"/> + </section> + <section name="algorithm"> + <param name="max_num_peaks_considered" value="400"/> + <section name="superimposer"> + <param name="mz_pair_max_distance" value="0.5"/> + <param name="rt_pair_distance_fraction" value="0.1"/> + <param name="num_used_points" value="2000"/> + <param name="scaling_bucket_size" value="0.005"/> + <param name="shift_bucket_size" value="3.0"/> + <param name="max_shift" value="1000.0"/> + <param name="max_scaling" value="2.0"/> + <param name="dump_buckets" value=""/> + <param name="dump_pairs" value=""/> + </section> + <section name="pairfinder"> + <param name="second_nearest_gap" value="2.0"/> + <param name="use_identifications" value="false"/> + <param name="ignore_charge" value="false"/> + <param name="ignore_adduct" value="true"/> + <section name="distance_RT"> + <param name="max_difference" value="100.0"/> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_MZ"> + <param name="max_difference" value="0.3"/> + <param name="unit" value="Da"/> + <param name="exponent" value="2.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_intensity"> + <param name="exponent" value="1.0"/> + <param name="weight" value="0.0"/> + <param name="log_transform" value="disabled"/> + </section> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/> + <output_collection name="out" count="2"/> + <section name="reference"> + <param name="file" value="MapAlignerPoseClustering_1_input1.featureXML"/> + <param name="index" value="0"/> + </section> + <section name="algorithm"> + <param name="max_num_peaks_considered" value="400"/> + <section name="superimposer"> + <param name="mz_pair_max_distance" value="0.5"/> + <param name="rt_pair_distance_fraction" value="0.1"/> + <param name="num_used_points" value="2000"/> + <param name="scaling_bucket_size" value="0.005"/> + <param name="shift_bucket_size" value="3.0"/> + <param name="max_shift" value="1000.0"/> + <param name="max_scaling" value="2.0"/> + <param name="dump_buckets" value=""/> + <param name="dump_pairs" value=""/> + </section> + <section name="pairfinder"> + <param name="second_nearest_gap" value="2.0"/> + <param name="use_identifications" value="false"/> + <param name="ignore_charge" value="true"/> + <param name="ignore_adduct" value="true"/> + <section name="distance_RT"> + <param name="max_difference" value="30.0"/> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_MZ"> + <param name="max_difference" value="0.3"/> + <param name="unit" value="Da"/> + <param name="exponent" value="2.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_intensity"> + <param name="exponent" value="1.0"/> + <param name="weight" value="0.0"/> + <param name="log_transform" value="disabled"/> + </section> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML"/> + <output_collection name="trafo_out" count="2"/> + <section name="reference"> + <param name="index" value="2"/> + </section> + <section name="algorithm"> + <param name="max_num_peaks_considered" value="400"/> + <section name="superimposer"> + <param name="mz_pair_max_distance" value="0.5"/> + <param name="rt_pair_distance_fraction" value="0.1"/> + <param name="num_used_points" value="2000"/> + <param name="scaling_bucket_size" value="0.005"/> + <param name="shift_bucket_size" value="3.0"/> + <param name="max_shift" value="1000.0"/> + <param name="max_scaling" value="2.0"/> + <param name="dump_buckets" value=""/> + <param name="dump_pairs" value=""/> + </section> + <section name="pairfinder"> + <param name="second_nearest_gap" value="2.0"/> + <param name="use_identifications" value="false"/> + <param name="ignore_charge" value="true"/> + <param name="ignore_adduct" value="true"/> + <section name="distance_RT"> + <param name="max_difference" value="30.0"/> + <param name="exponent" value="1.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_MZ"> + <param name="max_difference" value="0.3"/> + <param name="unit" value="Da"/> + <param name="exponent" value="2.0"/> + <param name="weight" value="1.0"/> + </section> + <section name="distance_intensity"> + <param name="exponent" value="1.0"/> + <param name="weight" value="0.0"/> + <param name="log_transform" value="disabled"/> + </section> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_MapAlignerSpectrum"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapAlignerSpectrum_1_input1.mzML,MapAlignerSpectrum_1_input2.mzML,MapAlignerSpectrum_1_input3.mzML"/> + <output_collection name="out" count="3"/> + <section name="algorithm"> + <param name="gapcost" value="1.0"/> + <param name="affinegapcost" value="0.5"/> + <param name="cutoff_score" value="0.7"/> + <param name="bucketsize" value="100"/> + <param name="anchorpoints" value="100"/> + <param name="mismatchscore" value="-5.0"/> + <param name="scorefunction" value="SteinScottImproveScore"/> + </section> + <section name="model"> + <param name="type" value="interpolated"/> + <section name="linear"> + <param name="symmetric_regression" value="false"/> + <param name="x_weight" value=""/> + <param name="y_weight" value=""/> + <param name="x_datum_min" value="1e-15"/> + <param name="x_datum_max" value="1000000000000000.0"/> + <param name="y_datum_min" value="1e-15"/> + <param name="y_datum_max" value="1000000000000000.0"/> + </section> + <section name="b_spline"> + <param name="wavelength" value="0.0"/> + <param name="num_nodes" value="5"/> + <param name="extrapolate" value="linear"/> + <param name="boundary_condition" value="2"/> + </section> + <section name="lowess"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + <section name="interpolated"> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="two-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_MapAlignerTreeGuided"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/> + <output_collection name="out" count="3"/> + <section name="algorithm"> + <param name="model_type" value="b_spline"/> + <section name="model"> + <param name="type" value="b_spline"/> + <section name="linear"> + <param name="symmetric_regression" value="false"/> + <param name="x_weight" value=""/> + <param name="y_weight" value=""/> + <param name="x_datum_min" value="1e-15"/> + <param name="x_datum_max" value="1000000000000000.0"/> + <param name="y_datum_min" value="1e-15"/> + <param name="y_datum_max" value="1000000000000000.0"/> + </section> + <section name="b_spline"> + <param name="wavelength" value="0.0"/> + <param name="num_nodes" value="5"/> + <param name="extrapolate" value="linear"/> + <param name="boundary_condition" value="2"/> + </section> + <section name="lowess"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + <section name="interpolated"> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="two-point-linear"/> + </section> + </section> + <section name="align_algorithm"> + <param name="score_cutoff" value="false"/> + <param name="min_score" value="0.05"/> + <param name="min_run_occur" value="2"/> + <param name="max_rt_shift" value="0.5"/> + <param name="use_unassigned_peptides" value="true"/> + <param name="use_feature_rt" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/> + <output_collection name="trafo_out" count="3"/> + <section name="algorithm"> + <param name="model_type" value="b_spline"/> + <section name="model"> + <param name="type" value="b_spline"/> + <section name="linear"> + <param name="symmetric_regression" value="false"/> + <param name="x_weight" value=""/> + <param name="y_weight" value=""/> + <param name="x_datum_min" value="1e-15"/> + <param name="x_datum_max" value="1000000000000000.0"/> + <param name="y_datum_min" value="1e-15"/> + <param name="y_datum_max" value="1000000000000000.0"/> + </section> + <section name="b_spline"> + <param name="wavelength" value="0.0"/> + <param name="num_nodes" value="5"/> + <param name="extrapolate" value="linear"/> + <param name="boundary_condition" value="2"/> + </section> + <section name="lowess"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + <section name="interpolated"> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="two-point-linear"/> + </section> + </section> + <section name="align_algorithm"> + <param name="score_cutoff" value="false"/> + <param name="min_score" value="0.05"/> + <param name="min_run_occur" value="2"/> + <param name="max_rt_shift" value="0.5"/> + <param name="use_unassigned_peptides" value="true"/> + <param name="use_feature_rt" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/> + <output_collection name="out" count="3"/> + <section name="algorithm"> + <param name="model_type" value="b_spline"/> + <section name="model"> + <param name="type" value="b_spline"/> + <section name="linear"> + <param name="symmetric_regression" value="false"/> + <param name="x_weight" value=""/> + <param name="y_weight" value=""/> + <param name="x_datum_min" value="1e-15"/> + <param name="x_datum_max" value="1000000000000000.0"/> + <param name="y_datum_min" value="1e-15"/> + <param name="y_datum_max" value="1000000000000000.0"/> + </section> + <section name="b_spline"> + <param name="wavelength" value="0.0"/> + <param name="num_nodes" value="5"/> + <param name="extrapolate" value="linear"/> + <param name="boundary_condition" value="2"/> + </section> + <section name="lowess"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + <section name="interpolated"> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="two-point-linear"/> + </section> + </section> + <section name="align_algorithm"> + <param name="score_cutoff" value="false"/> + <param name="min_score" value="0.05"/> + <param name="min_run_occur" value="2"/> + <param name="max_rt_shift" value="0.5"/> + <param name="use_unassigned_peptides" value="true"/> + <param name="use_feature_rt" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_MapNormalizer"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapNormalizer_input.mzML"/> + <output name="out" file="MapNormalizer.tmp" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_MapRTTransformer"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapRTTransformer_1_input.featureXML"/> + <output name="out" file="MapRTTransformer_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/> + <param name="invert" value="false"/> + <param name="store_original_rt" value="false"/> + <section name="model"> + <param name="type" value="none"/> + <section name="linear"> + <param name="symmetric_regression" value="false"/> + <param name="x_weight" value=""/> + <param name="y_weight" value=""/> + <param name="x_datum_min" value="1e-15"/> + <param name="x_datum_max" value="1000000000000000.0"/> + <param name="y_datum_min" value="1e-15"/> + <param name="y_datum_max" value="1000000000000000.0"/> + </section> + <section name="b_spline"> + <param name="wavelength" value="0.0"/> + <param name="num_nodes" value="5"/> + <param name="extrapolate" value="linear"/> + <param name="boundary_condition" value="2"/> + </section> + <section name="lowess"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + <section name="interpolated"> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="two-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapRTTransformer_2_input.mzML"/> + <output name="out" file="MapRTTransformer_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/> + <param name="invert" value="false"/> + <param name="store_original_rt" value="false"/> + <section name="model"> + <param name="type" value="none"/> + <section name="linear"> + <param name="symmetric_regression" value="false"/> + <param name="x_weight" value=""/> + <param name="y_weight" value=""/> + <param name="x_datum_min" value="1e-15"/> + <param name="x_datum_max" value="1000000000000000.0"/> + <param name="y_datum_min" value="1e-15"/> + <param name="y_datum_max" value="1000000000000000.0"/> + </section> + <section name="b_spline"> + <param name="wavelength" value="0.0"/> + <param name="num_nodes" value="5"/> + <param name="extrapolate" value="linear"/> + <param name="boundary_condition" value="2"/> + </section> + <section name="lowess"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + <section name="interpolated"> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="two-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="trafo_in" value="MapAlignerPoseClustering_1_trafo2.trafoXML"/> + <output name="trafo_out" file="MapRTTransformer_3_trafo.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> + <param name="invert" value="true"/> + <param name="store_original_rt" value="false"/> + <section name="model"> + <param name="type" value="none"/> + <section name="linear"> + <param name="symmetric_regression" value="false"/> + <param name="x_weight" value=""/> + <param name="y_weight" value=""/> + <param name="x_datum_min" value="1e-15"/> + <param name="x_datum_max" value="1000000000000000.0"/> + <param name="y_datum_min" value="1e-15"/> + <param name="y_datum_max" value="1000000000000000.0"/> + </section> + <section name="b_spline"> + <param name="wavelength" value="0.0"/> + <param name="num_nodes" value="5"/> + <param name="extrapolate" value="linear"/> + <param name="boundary_condition" value="2"/> + </section> + <section name="lowess"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + <section name="interpolated"> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="two-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapRTTransformer_4_input.chrom.mzML"/> + <output name="out" file="MapRTTransformer_4_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/> + <param name="invert" value="false"/> + <param name="store_original_rt" value="false"/> + <section name="model"> + <param name="type" value="none"/> + <section name="linear"> + <param name="symmetric_regression" value="false"/> + <param name="x_weight" value=""/> + <param name="y_weight" value=""/> + <param name="x_datum_min" value="1e-15"/> + <param name="x_datum_max" value="1000000000000000.0"/> + <param name="y_datum_min" value="1e-15"/> + <param name="y_datum_max" value="1000000000000000.0"/> + </section> + <section name="b_spline"> + <param name="wavelength" value="0.0"/> + <param name="num_nodes" value="5"/> + <param name="extrapolate" value="linear"/> + <param name="boundary_condition" value="2"/> + </section> + <section name="lowess"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + <section name="interpolated"> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="two-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapRTTransformer_1_input.featureXML"/> + <output name="out" file="MapRTTransformer_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="trafo_in" value="MapRTTransformer_trafo_none.trafoXML"/> + <param name="invert" value="false"/> + <param name="store_original_rt" value="false"/> + <section name="model"> + <param name="type" value="none"/> + <section name="linear"> + <param name="symmetric_regression" value="false"/> + <param name="x_weight" value=""/> + <param name="y_weight" value=""/> + <param name="x_datum_min" value="1e-15"/> + <param name="x_datum_max" value="1000000000000000.0"/> + <param name="y_datum_min" value="1e-15"/> + <param name="y_datum_max" value="1000000000000000.0"/> + </section> + <section name="b_spline"> + <param name="wavelength" value="0.0"/> + <param name="num_nodes" value="5"/> + <param name="extrapolate" value="linear"/> + <param name="boundary_condition" value="2"/> + </section> + <section name="lowess"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + <section name="interpolated"> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="two-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapRTTransformer_1_input.featureXML"/> + <output name="out" file="MapRTTransformer_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/> + <param name="invert" value="false"/> + <param name="store_original_rt" value="true"/> + <section name="model"> + <param name="type" value="none"/> + <section name="linear"> + <param name="symmetric_regression" value="false"/> + <param name="x_weight" value=""/> + <param name="y_weight" value=""/> + <param name="x_datum_min" value="1e-15"/> + <param name="x_datum_max" value="1000000000000000.0"/> + <param name="y_datum_min" value="1e-15"/> + <param name="y_datum_max" value="1000000000000000.0"/> + </section> + <section name="b_spline"> + <param name="wavelength" value="0.0"/> + <param name="num_nodes" value="5"/> + <param name="extrapolate" value="linear"/> + <param name="boundary_condition" value="2"/> + </section> + <section name="lowess"> + <param name="span" value="0.666666666666667"/> + <param name="num_iterations" value="3"/> + <param name="delta" value="-1.0"/> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="four-point-linear"/> + </section> + <section name="interpolated"> + <param name="interpolation_type" value="cspline"/> + <param name="extrapolation_type" value="two-point-linear"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_MapStatistics"> +</xml> + <xml name="autotest_MaRaClusterAdapter"/> + <xml name="autotest_MascotAdapterOnline"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="keep_protein_links" value="true"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="spectra_comet.mzML"/> + <output name="out" file="MascotAdapterOnline_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <section name="Mascot_parameters"> + <param name="database" value="SwissProt"/> + <param name="search_type" value="MIS"/> + <param name="enzyme" value="Trypsin"/> + <param name="instrument" value="Default"/> + <param name="missed_cleavages" value="1"/> + <param name="precursor_mass_tolerance" value="3.0"/> + <param name="precursor_error_units" value="Da"/> + <param name="fragment_mass_tolerance" value="0.3"/> + <param name="fragment_error_units" value="Da"/> + <param name="charges" value="1,2,3"/> + <param name="taxonomy" value="All entries"/> + <param name="fixed_modifications" value=""/> + <param name="variable_modifications" value=""/> + <param name="special_modifications" value="Cation:Na (DE),Deamidated (NQ),Oxidation (HW),Phospho (ST),Sulfo (ST)"/> + <param name="mass_type" value="monoisotopic"/> + <param name="number_of_hits" value="0"/> + <param name="skip_spectrum_charges" value="false"/> + <param name="search_title" value="OpenMS_search"/> + <param name="username" value="OpenMS"/> + <param name="email" value="openmsjenkins@gmail.com"/> + </section> + <section name="Mascot_server"> + <param name="hostname" value="www.matrixscience.com"/> + <param name="host_port" value="80"/> + <param name="server_path" value=""/> + <param name="timeout" value="1500"/> + <param name="boundary" value="GZWgAaYKjHFeUaLOLEIOMq"/> + <param name="use_proxy" value="false"/> + <param name="proxy_host" value=""/> + <param name="proxy_port" value="0"/> + <param name="proxy_username" value=""/> + <param name="proxy_password" value=""/> + <param name="login" value="false"/> + <param name="username" value=""/> + <param name="password" value=""/> + <param name="use_ssl" value="false"/> + <param name="export_params" value="_ignoreionsscorebelow=0&_sigthreshold=0.99&_showsubsets=1&show_same_sets=1&report=0&percolate=0&query_master=0"/> + <param name="skip_export" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_MascotAdapter"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MascotAdapter_1_input.mzData"/> + <output name="out" file="MascotAdapter_1_output.mascot_in" compare="sim_size" delta="5700"/> + <param name="out_type" value="mgf"/> + <param name="instrument" value="ESI-TRAP"/> + <param name="precursor_mass_tolerance" value="1.3"/> + <param name="peak_mass_tolerance" value="0.3"/> + <param name="taxonomy" value=". . . . . . Chordata (vertebrates and relatives)"/> + <param name="modifications" value=""Carboxymethyl (C)""/> + <param name="variable_modifications" value=""Variable_Modifications_TEST_1""/> + <param name="charges" value=""1+" "2+" "3+""/> + <param name="db" value="MSDB"/> + <param name="hits" value="AUTO"/> + <param name="cleavage" value="Trypsin"/> + <param name="missed_cleavages" value="1"/> + <param name="sig_threshold" value="0.05"/> + <param name="pep_homol" value="1.0"/> + <param name="pep_ident" value="1.0"/> + <param name="pep_rank" value="1"/> + <param name="prot_score" value="1.0"/> + <param name="pep_score" value="1.0"/> + <param name="pep_exp_z" value="1"/> + <param name="show_unassigned" value="1"/> + <param name="first_dim_rt" value="0.0"/> + <param name="boundary" value="ABCDEFGHIJKMNOPQRSTUVWXYZ"/> + <param name="mass_type" value="Monoisotopic"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MascotAdapter_2_input.mascotXML"/> + <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="instrument" value="Default"/> + <param name="precursor_mass_tolerance" value="2.0"/> + <param name="peak_mass_tolerance" value="1.0"/> + <param name="taxonomy" value="All entries"/> + <param name="modifications" value=""/> + <param name="variable_modifications" value=""/> + <param name="charges" value=""1+" "2+" "3+""/> + <param name="db" value="MSDB"/> + <param name="hits" value="AUTO"/> + <param name="cleavage" value="Trypsin"/> + <param name="missed_cleavages" value="0"/> + <param name="sig_threshold" value="0.05"/> + <param name="pep_homol" value="1.0"/> + <param name="pep_ident" value="1.0"/> + <param name="pep_rank" value="1"/> + <param name="prot_score" value="1.0"/> + <param name="pep_score" value="1.0"/> + <param name="pep_exp_z" value="1"/> + <param name="show_unassigned" value="1"/> + <param name="first_dim_rt" value="0.0"/> + <param name="boundary" value=""/> + <param name="mass_type" value="Monoisotopic"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_MassCalculator"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MassCalculator_1_input.tsv" ftype="tabular"/> + <param name="in_seq" value=""/> + <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta="5700" ftype="csv"/> + <param name="charge" value="0 1"/> + <param name="format" value="table"/> + <param name="average_mass" value="false"/> + <param name="fragment_type" value="full"/> + <param name="separator" value=","/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in_seq" value=""LDQWLC(Carbamidomethyl)EKL" "(Glu->pyro-Glu)EAM(Oxidation)APKHK" "RANVM(Oxidation)DYR" "FGVEQDVDMVFASFIR""/> + <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta="5700" ftype="csv"/> + <param name="charge" value="1 2 3"/> + <param name="format" value="list"/> + <param name="average_mass" value="false"/> + <param name="fragment_type" value="full"/> + <param name="separator" value=""/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_MassTraceExtractor"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MassTraceExtractor_1_input.mzML"/> + <output name="out" file="MassTraceExtractor_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="out_type" value="featurexml"/> + <section name="algorithm"> + <section name="common"> + <param name="noise_threshold_int" value="10.0"/> + <param name="chrom_peak_snr" value="3.0"/> + <param name="chrom_fwhm" value="5.0"/> + </section> + <section name="mtd"> + <param name="mass_error_ppm" value="20.0"/> + <param name="reestimate_mt_sd" value="true"/> + <param name="quant_method" value="area"/> + <param name="trace_termination_criterion" value="outlier"/> + <param name="trace_termination_outliers" value="5"/> + <param name="min_sample_rate" value="0.5"/> + <param name="min_trace_length" value="5.0"/> + <param name="max_trace_length" value="-1.0"/> + </section> + <section name="epd"> + <param name="width_filtering" value="off"/> + <param name="min_fwhm" value="3.0"/> + <param name="max_fwhm" value="60.0"/> + <param name="masstrace_snr_filtering" value="false"/> + <param name="enabled" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MassTraceExtractor_1_input.mzML"/> + <output name="out" file="MassTraceExtractor_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="out_type" value="featurexml"/> + <section name="algorithm"> + <section name="common"> + <param name="noise_threshold_int" value="10.0"/> + <param name="chrom_peak_snr" value="3.0"/> + <param name="chrom_fwhm" value="5.0"/> + </section> + <section name="mtd"> + <param name="mass_error_ppm" value="20.0"/> + <param name="reestimate_mt_sd" value="true"/> + <param name="quant_method" value="area"/> + <param name="trace_termination_criterion" value="outlier"/> + <param name="trace_termination_outliers" value="5"/> + <param name="min_sample_rate" value="0.5"/> + <param name="min_trace_length" value="6.0"/> + <param name="max_trace_length" value="12.0"/> + </section> + <section name="epd"> + <param name="width_filtering" value="off"/> + <param name="min_fwhm" value="3.0"/> + <param name="max_fwhm" value="60.0"/> + <param name="masstrace_snr_filtering" value="false"/> + <param name="enabled" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_MetaboliteAdductDecharger"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/> + <output name="out_fm" file="MetaboliteAdductDecharger_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <section name="algorithm"> + <section name="MetaboliteFeatureDeconvolution"> + <param name="charge_min" value="1"/> + <param name="charge_max" value="3"/> + <param name="charge_span_max" value="3"/> + <param name="q_try" value="feature"/> + <param name="retention_max_diff" value="1.0"/> + <param name="retention_max_diff_local" value="1.0"/> + <param name="mass_max_diff" value="0.05"/> + <param name="unit" value="Da"/> + <param name="potential_adducts" value=""H:+:0.4" "Na:+:0.25" "NH4:+:0.25" "K:+:0.1" "H-2O-1:0:0.05""/> + <param name="max_neutrals" value="1"/> + <param name="use_minority_bound" value="true"/> + <param name="max_minority_bound" value="3"/> + <param name="min_rt_overlap" value="0.66"/> + <param name="intensity_filter" value="false"/> + <param name="negative_mode" value="false"/> + <param name="default_map_label" value="decharged features"/> + <param name="verbose_level" value="0"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/> + <output name="out_cm" file="MetaboliteAdductDecharger_2_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <output name="outpairs" file="MetaboliteAdductDecharger_2_output_2.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="algorithm"> + <section name="MetaboliteFeatureDeconvolution"> + <param name="charge_min" value="1"/> + <param name="charge_max" value="3"/> + <param name="charge_span_max" value="3"/> + <param name="q_try" value="feature"/> + <param name="retention_max_diff" value="1.0"/> + <param name="retention_max_diff_local" value="1.0"/> + <param name="mass_max_diff" value="0.05"/> + <param name="unit" value="Da"/> + <param name="potential_adducts" value=""H:+:0.4" "Na:+:0.25" "NH4:+:0.25" "K:+:0.1" "H-2O-1:0:0.05""/> + <param name="max_neutrals" value="1"/> + <param name="use_minority_bound" value="true"/> + <param name="max_minority_bound" value="3"/> + <param name="min_rt_overlap" value="0.66"/> + <param name="intensity_filter" value="false"/> + <param name="negative_mode" value="false"/> + <param name="default_map_label" value="decharged features"/> + <param name="verbose_level" value="0"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_cm_FLAG,outpairs_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_MetaboliteSpectralMatcher"> +</xml> + <xml name="autotest_MetaProSIP"> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="min_correlation_distance_to_averagine" value="-1.0"/> + <param name="pattern_15N_TIC_threshold" value="0.95"/> + <param name="pattern_13C_TIC_threshold" value="0.95"/> + <param name="pattern_2H_TIC_threshold" value="0.95"/> + <param name="pattern_18O_TIC_threshold" value="0.95"/> + <param name="heatmap_bins" value="20"/> + <param name="observed_peak_fraction" value="0.5"/> + <param name="min_consecutive_isotopes" value="2"/> + <param name="score_plot_yaxis_min" value="0.0"/> + <param name="collect_method" value="correlation_maximum"/> + <param name="lowRIA_correlation_threshold" value="-1.0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in_mzML" value="MetaProSIP_1_input.mzML"/> + <param name="in_fasta" value="MetaProSIP_1_input.fasta"/> + <output name="out_csv" file="MetaProSIP_1_output_1.csv" compare="sim_size" delta="5700" ftype="csv"/> + <output name="out_peptide_centric_csv" file="MetaProSIP_1_output_2.csv" compare="sim_size" delta="5700" ftype="csv"/> + <param name="in_featureXML" value="MetaProSIP_1_input.featureXML"/> + <param name="mz_tolerance_ppm" value="10.0"/> + <param name="rt_tolerance_s" value="30.0"/> + <param name="intensity_threshold" value="10.0"/> + <param name="correlation_threshold" value="0.7"/> + <param name="xic_threshold" value="0.7"/> + <param name="decomposition_threshold" value="0.7"/> + <param name="weight_merge_window" value="5.0"/> + <param name="plot_extension" value="png"/> + <param name="qc_output_directory" value=""/> + <param name="labeling_element" value="C"/> + <param name="use_unassigned_ids" value="false"/> + <param name="use_averagine_ids" value="false"/> + <param name="report_natural_peptides" value="false"/> + <param name="filter_monoisotopic" value="false"/> + <param name="cluster" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_MRMMapper"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MRMMapping_input.chrom.mzML"/> + <param name="tr" value="MRMMapping_input.TraML"/> + <output name="out" file="MRMMapping_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="precursor_tolerance" value="0.3"/> + <param name="product_tolerance" value="0.3"/> + <param name="map_multiple_assays" value="false"/> + <param name="error_on_unmapped" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MRMMapping_input.chrom.mzML"/> + <param name="tr" value="MRMMapping_input_2.TraML"/> + <output name="out" file="MRMMapping_output_2.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="precursor_tolerance" value="0.01"/> + <param name="product_tolerance" value="0.01"/> + <param name="map_multiple_assays" value="false"/> + <param name="error_on_unmapped" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_MRMPairFinder"> +</xml> + <xml name="autotest_MRMTransitionGroupPicker"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/> + <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/> + <output name="out" file="MRMTransitionGroupPicker_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <section name="algorithm"> + <param name="stop_after_feature" value="-1"/> + <param name="stop_after_intensity_ratio" value="0.0001"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="false"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="1.0"/> + <param name="minimal_quality" value="-10000.0"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="15"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="50.0"/> + <param name="use_gauss" value="true"/> + <param name="peak_width" value="40.0"/> + <param name="signal_to_noise" value="1.0"/> + <param name="sn_win_len" value="1000.0"/> + <param name="sn_bin_count" value="30"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="legacy"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/> + <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/> + <output name="out" file="MRMTransitionGroupPicker_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <section name="algorithm"> + <param name="stop_after_feature" value="-1"/> + <param name="stop_after_intensity_ratio" value="0.0001"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="false"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="1.0"/> + <param name="minimal_quality" value="-10000.0"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="true"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="15"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="50.0"/> + <param name="use_gauss" value="true"/> + <param name="peak_width" value="40.0"/> + <param name="signal_to_noise" value="1.0"/> + <param name="sn_win_len" value="1000.0"/> + <param name="sn_bin_count" value="30"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="legacy"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_MSFraggerAdapter"/> + <xml name="autotest_MSGFPlusAdapter"> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="add_decoys" value="false"/> + <param name="legacy_conversion" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="spectra.mzML"/> + <output name="out" file="MSGFPlusAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <output name="mzid_out" file="MSGFPlusAdapter_1_out2.tmp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> + <param name="database" value="proteins.fasta"/> + <param name="precursor_mass_tolerance" value="10.0"/> + <param name="precursor_error_units" value="ppm"/> + <param name="isotope_error_range" value="0,1"/> + <param name="fragment_method" value="from_spectrum"/> + <param name="instrument" value="high_res"/> + <param name="enzyme" value="Trypsin/P"/> + <param name="protocol" value="none"/> + <param name="tryptic" value="fully"/> + <param name="min_precursor_charge" value="1"/> + <param name="max_precursor_charge" value="3"/> + <param name="min_peptide_length" value="6"/> + <param name="max_peptide_length" value="40"/> + <param name="matches_per_spec" value="1"/> + <param name="add_features" value="false"/> + <param name="max_mods" value="2"/> + <param name="max_missed_cleavages" value="-1"/> + <param name="tasks" value="0"/> + <param name="fixed_modifications" value=""/> + <param name="variable_modifications" value="Oxidation (M)"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mzid_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_MSSimulator"> +</xml> + <xml name="autotest_MSstatsConverter"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="retention_time_summarization_method" value="max"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MSstatsConverter_1_in.consensusXML"/> + <param name="in_design" value="MSstatsConverter_1_design.tsv" ftype="tabular"/> + <param name="method" value="LFQ"/> + <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/> + <param name="msstats_condition" value="MSstats_Condition"/> + <param name="msstats_mixture" value="MSstats_Mixture"/> + <param name="labeled_reference_peptides" value="false"/> + <output name="out" file="MSstatsConverter_1_out.csv" compare="sim_size" delta="5700" ftype="csv"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="retention_time_summarization_method" value="manual"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MSstatsConverter_2_in.consensusXML"/> + <param name="in_design" value="MSstatsConverter_2_design.tsv" ftype="tabular"/> + <param name="method" value="ISO"/> + <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/> + <param name="msstats_condition" value="MSstats_Condition"/> + <param name="msstats_mixture" value="MSstats_Mixture"/> + <param name="labeled_reference_peptides" value="false"/> + <output name="out" file="MSstatsConverter_2_out.csv" compare="sim_size" delta="5700" ftype="csv"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="retention_time_summarization_method" value="manual"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MSstatsConverter_3_in.consensusXML"/> + <param name="in_design" value="MSstatsConverter_3_design.tsv" ftype="tabular"/> + <param name="method" value="ISO"/> + <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/> + <param name="msstats_condition" value="MSstats_Condition"/> + <param name="msstats_mixture" value="MSstats_Mixture"/> + <param name="labeled_reference_peptides" value="false"/> + <output name="out" file="MSstatsConverter_3_out.csv" compare="sim_size" delta="5700" ftype="csv"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_MultiplexResolver"> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MultiplexResolver_1_input.consensusXML"/> + <output name="out" file="MultiplexResolver_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <output name="out_conflicts" file="MultiplexResolver_1_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="algorithm"> + <param name="labels" value="[][Lys4,Arg6][Lys8,Arg10]"/> + <param name="missed_cleavages" value="1"/> + <param name="mass_tolerance" value="0.1"/> + <param name="mz_tolerance" value="10"/> + <param name="rt_tolerance" value="5"/> + </section> + <section name="labels"> + <param name="Arg6" value="6.0201290268"/> + <param name="Arg10" value="10.0082686"/> + <param name="Lys4" value="4.0251069836"/> + <param name="Lys6" value="6.0201290268"/> + <param name="Lys8" value="8.0141988132"/> + <param name="Leu3" value="3.01883"/> + <param name="Dimethyl0" value="28.0313"/> + <param name="Dimethyl4" value="32.056407"/> + <param name="Dimethyl6" value="34.063117"/> + <param name="Dimethyl8" value="36.07567"/> + <param name="ICPL0" value="105.021464"/> + <param name="ICPL4" value="109.046571"/> + <param name="ICPL6" value="111.041593"/> + <param name="ICPL10" value="115.0667"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MultiplexResolver_2_input.consensusXML"/> + <output name="out" file="MultiplexResolver_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <output name="out_conflicts" file="MultiplexResolver_2_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="algorithm"> + <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/> + <param name="missed_cleavages" value="4"/> + <param name="mass_tolerance" value="0.1"/> + <param name="mz_tolerance" value="10"/> + <param name="rt_tolerance" value="5"/> + </section> + <section name="labels"> + <param name="Arg6" value="6.0201290268"/> + <param name="Arg10" value="10.0082686"/> + <param name="Lys4" value="4.0251069836"/> + <param name="Lys6" value="6.0201290268"/> + <param name="Lys8" value="8.0141988132"/> + <param name="Leu3" value="3.01883"/> + <param name="Dimethyl0" value="28.0313"/> + <param name="Dimethyl4" value="32.056407"/> + <param name="Dimethyl6" value="34.063117"/> + <param name="Dimethyl8" value="36.07567"/> + <param name="ICPL0" value="105.021464"/> + <param name="ICPL4" value="109.046571"/> + <param name="ICPL6" value="111.041593"/> + <param name="ICPL10" value="115.0667"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MultiplexResolver_3_input.consensusXML"/> + <output name="out" file="MultiplexResolver_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <output name="out_conflicts" file="MultiplexResolver_3_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="algorithm"> + <param name="labels" value="[][Leu3]"/> + <param name="missed_cleavages" value="2"/> + <param name="mass_tolerance" value="0.1"/> + <param name="mz_tolerance" value="10"/> + <param name="rt_tolerance" value="5"/> + </section> + <section name="labels"> + <param name="Arg6" value="6.0201290268"/> + <param name="Arg10" value="10.0082686"/> + <param name="Lys4" value="4.0251069836"/> + <param name="Lys6" value="6.0201290268"/> + <param name="Lys8" value="8.0141988132"/> + <param name="Leu3" value="3.01883"/> + <param name="Dimethyl0" value="28.0313"/> + <param name="Dimethyl4" value="32.056407"/> + <param name="Dimethyl6" value="34.063117"/> + <param name="Dimethyl8" value="36.07567"/> + <param name="ICPL0" value="105.021464"/> + <param name="ICPL4" value="109.046571"/> + <param name="ICPL6" value="111.041593"/> + <param name="ICPL10" value="115.0667"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MultiplexResolver_4_input.consensusXML"/> + <param name="in_blacklist" value="MultiplexResolver_4_input.mzML"/> + <output name="out" file="MultiplexResolver_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <output name="out_conflicts" file="MultiplexResolver_4_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <section name="algorithm"> + <param name="labels" value="[Dimethyl0][Dimethyl6]"/> + <param name="missed_cleavages" value="3"/> + <param name="mass_tolerance" value="0.1"/> + <param name="mz_tolerance" value="10"/> + <param name="rt_tolerance" value="10"/> + </section> + <section name="labels"> + <param name="Arg6" value="6.0201290268"/> + <param name="Arg10" value="10.0082686"/> + <param name="Lys4" value="4.0251069836"/> + <param name="Lys6" value="6.0201290268"/> + <param name="Lys8" value="8.0141988132"/> + <param name="Leu3" value="3.01883"/> + <param name="Dimethyl0" value="28.0313"/> + <param name="Dimethyl4" value="32.056407"/> + <param name="Dimethyl6" value="34.063117"/> + <param name="Dimethyl8" value="36.07567"/> + <param name="ICPL0" value="105.021464"/> + <param name="ICPL4" value="109.046571"/> + <param name="ICPL6" value="111.041593"/> + <param name="ICPL10" value="115.0667"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_MyriMatchAdapter"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="MinPeptideMass" value="0.0"/> + <param name="MaxPeptideMass" value="10000.0"/> + <param name="MinPeptideLength" value="5"/> + <param name="MaxPeptideLength" value="75"/> + <param name="UseSmartPlusThreeModel" value="false"/> + <param name="NumIntensityClasses" value="3"/> + <param name="ClassSizeMultiplier" value="2.0"/> + <param name="MonoisotopeAdjustmentSet" value="[-1,2]"/> + <param name="SpectrumListFilters" value=""/> + <param name="ignoreConfigErrors" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="spectra.mzML"/> + <output name="out" file="MyriMatchAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="precursor_mass_tolerance" value="5.0"/> + <param name="precursor_mass_tolerance_unit" value="ppm"/> + <param name="precursor_mass_tolerance_avg" value="false"/> + <param name="fragment_mass_tolerance" value="0.3"/> + <param name="fragment_mass_tolerance_unit" value="Da"/> + <param name="database" value="proteins.fasta"/> + <param name="fixed_modifications" value=""/> + <param name="variable_modifications" value="Oxidation (M)"/> + <param name="NumChargeStates" value="3"/> + <param name="TicCutoffPercentage" value="0.98"/> + <param name="MaxDynamicMods" value="2"/> + <param name="MaxResultRank" value="5"/> + <param name="CleavageRules" value=""/> + <param name="MinTerminiCleavages" value="2"/> + <param name="MaxMissedCleavages" value="-1"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_MzMLSplitter"/> + <xml name="autotest_MzTabExporter"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="first_run_inference_only" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MzTabExporter_1_input.consensusXML"/> + <output name="out" file="MzTabExporter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> + <param name="opt_columns" value="subfeatures"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="first_run_inference_only" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MzTabExporter_2_input.idXML"/> + <output name="out" file="MzTabExporter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> + <param name="opt_columns" value="subfeatures"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="first_run_inference_only" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MzTabExporter_3_input.featureXML"/> + <output name="out" file="MzTabExporter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> + <param name="opt_columns" value="subfeatures"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="first_run_inference_only" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="Epifany_2_out.consensusXML"/> + <output name="out" file="MzTabExporter_4_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> + <param name="opt_columns" value="subfeatures"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="first_run_inference_only" value="true"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MzTabExporter_5_in.consensusXML"/> + <output name="out" file="MzTabExporter_5_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> + <param name="opt_columns" value="subfeatures"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="first_run_inference_only" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MzTabExporter_6_input.idXML"/> + <output name="out" file="MzTabExporter_6_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> + <param name="opt_columns" value="subfeatures"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="first_run_inference_only" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MzTabExporter_7_input.consensusXML"/> + <output name="out" file="MzTabExporter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> + <param name="opt_columns" value="subfeatures"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_NoiseFilterGaussian"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="processOption" value="inmemory"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="NoiseFilterGaussian_1_input.mzML"/> + <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="gaussian_width" value="1.0"/> + <param name="ppm_tolerance" value="10.0"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="processOption" value="inmemory"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/> + <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="gaussian_width" value="50.0"/> + <param name="ppm_tolerance" value="10.0"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="processOption" value="lowmemory"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="NoiseFilterGaussian_1_input.mzML"/> + <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="gaussian_width" value="1.0"/> + <param name="ppm_tolerance" value="10.0"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="processOption" value="lowmemory"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/> + <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="gaussian_width" value="50.0"/> + <param name="ppm_tolerance" value="10.0"/> + <param name="use_ppm_tolerance" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_NoiseFilterSGolay"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="processOption" value="inmemory"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="NoiseFilterSGolay_1_input.mzML"/> + <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="frame_length" value="9"/> + <param name="polynomial_order" value="4"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="processOption" value="inmemory"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/> + <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="frame_length" value="11"/> + <param name="polynomial_order" value="4"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="processOption" value="lowmemory"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="NoiseFilterSGolay_1_input.mzML"/> + <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="frame_length" value="9"/> + <param name="polynomial_order" value="4"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="processOption" value="lowmemory"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/> + <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="frame_length" value="11"/> + <param name="polynomial_order" value="4"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_NovorAdapter"/> + <xml name="autotest_NucleicAcidSearchEngine"> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="decharge_ms2" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="NucleicAcidSearchEngine_1.mzML"/> + <param name="database" value="NucleicAcidSearchEngine_1.fasta"/> + <output name="out" file="NucleicAcidSearchEngine_12_out.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> + <output name="id_out" file="NucleicAcidSearchEngine_11_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <section name="precursor"> + <param name="mass_tolerance" value="5.0"/> + <param name="mass_tolerance_unit" value="ppm"/> + <param name="min_charge" value="-2"/> + <param name="max_charge" value="-14"/> + <param name="include_unknown_charge" value="true"/> + <param name="use_avg_mass" value="false"/> + <param name="use_adducts" value="false"/> + <param name="potential_adducts" value=""K:+" "Na:+" "Na2:++" "K2:++" "NaK:++" "K3:+++" "Na3:+++" "NaK2:+++" "Na2K:+++""/> + <param name="isotopes" value="0 1 2"/> + </section> + <section name="fragment"> + <param name="mass_tolerance" value="5.0"/> + <param name="mass_tolerance_unit" value="ppm"/> + <param name="ions" value="a-B,c,w,y"/> + </section> + <section name="modifications"> + <param name="variable" value=""/> + <param name="variable_max_per_oligo" value="2"/> + <param name="resolve_ambiguities" value="false"/> + </section> + <section name="oligo"> + <param name="min_size" value="5"/> + <param name="max_size" value="0"/> + <param name="missed_cleavages" value="22"/> + <param name="enzyme" value="no cleavage"/> + </section> + <section name="report"> + <param name="top_hits" value="1"/> + </section> + <section name="fdr"> + <param name="decoy_pattern" value="DECOY_"/> + <param name="cutoff" value="0.05"/> + <param name="remove_decoys" value="true"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,id_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_OMSSAAdapter"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="pc" value="1"/> + <param name="hs" value="4"/> + <param name="tez" value="1"/> + <param name="tom" value="0"/> + <param name="tem" value="0"/> + <param name="tex" value="1446.94"/> + <param name="zt" value="3"/> + <param name="z1" value="0.95"/> + <param name="zc" value="1"/> + <param name="zcc" value="2"/> + <param name="zoh" value="2"/> + <param name="no" value="4"/> + <param name="nox" value="40"/> + <param name="i" value="1,4"/> + <param name="sp" value="100"/> + <param name="sb1" value="1"/> + <param name="sct" value="0"/> + <param name="x" value="0"/> + <param name="hm" value="2"/> + <param name="ht" value="6"/> + <param name="mm" value="128"/> + <param name="mnm" value="false"/> + <param name="is" value="0.0"/> + <param name="ir" value="0.0"/> + <param name="ii" value="0.0"/> + <param name="chunk_size" value="0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="spectra.mzML"/> + <output name="out" file="OMSSAAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="precursor_mass_tolerance" value="5.0"/> + <param name="precursor_error_units" value="ppm"/> + <param name="fragment_mass_tolerance" value="0.3"/> + <param name="database" value="proteins.fasta"/> + <param name="min_precursor_charge" value="1"/> + <param name="max_precursor_charge" value="3"/> + <param name="fixed_modifications" value=""/> + <param name="variable_modifications" value="Oxidation (M)"/> + <param name="v" value="1"/> + <param name="enzyme" value="Trypsin"/> + <param name="hl" value="30"/> + <param name="he" value="1.0"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_OpenPepXLLF"> + <test expect_num_outputs="5"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenPepXLLF_input.mzML"/> + <param name="database" value="OpenPepXLLF_input.fasta"/> + <param name="decoy_string" value="decoy"/> + <param name="decoy_prefix" value="true"/> + <output name="out_idXML" file="OpenPepXLLF_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <output name="out_mzIdentML" file="OpenPepXLLF_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/> + <output name="out_xquestxml" file="OpenPepXLLF_output.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> + <output name="out_xquest_specxml" file="OpenPepXLLF_output.spec.xml" compare="sim_size" delta="5700" ftype="spec.xml"/> + <section name="precursor"> + <param name="mass_tolerance" value="10.0"/> + <param name="mass_tolerance_unit" value="ppm"/> + <param name="min_charge" value="3"/> + <param name="max_charge" value="7"/> + <param name="corrections" value="2 1 0"/> + </section> + <section name="fragment"> + <param name="mass_tolerance" value="20.0"/> + <param name="mass_tolerance_xlinks" value="20.0"/> + <param name="mass_tolerance_unit" value="ppm"/> + </section> + <section name="modifications"> + <param name="fixed" value=""/> + <param name="variable" value=""/> + <param name="variable_max_per_peptide" value="2"/> + </section> + <section name="peptide"> + <param name="min_size" value="5"/> + <param name="missed_cleavages" value="2"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="cross_linker"> + <param name="residue1" value=""K" "N-term""/> + <param name="residue2" value=""K" "N-term""/> + <param name="mass" value="138.0680796"/> + <param name="mass_mono_link" value="156.07864431 155.094628715"/> + <param name="name" value="DSS"/> + </section> + <section name="algorithm"> + <param name="number_top_hits" value="5"/> + <param name="deisotope" value="auto"/> + <param name="use_sequence_tags" value="false"/> + <param name="sequence_tag_min_length" value="2"/> + </section> + <section name="ions"> + <param name="b_ions" value="true"/> + <param name="y_ions" value="true"/> + <param name="a_ions" value="false"/> + <param name="x_ions" value="false"/> + <param name="c_ions" value="false"/> + <param name="z_ions" value="false"/> + <param name="neutral_losses" value="true"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquestxml_FLAG,out_xquest_specxml_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenPepXLLF_input2.mzML"/> + <param name="database" value="OpenPepXLLF_input2.fasta"/> + <param name="decoy_string" value="decoy_"/> + <param name="decoy_prefix" value="true"/> + <output name="out_idXML" file="OpenPepXLLF_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <section name="precursor"> + <param name="mass_tolerance" value="10.0"/> + <param name="mass_tolerance_unit" value="ppm"/> + <param name="min_charge" value="3"/> + <param name="max_charge" value="7"/> + <param name="corrections" value="1 0"/> + </section> + <section name="fragment"> + <param name="mass_tolerance" value="0.2"/> + <param name="mass_tolerance_xlinks" value="0.3"/> + <param name="mass_tolerance_unit" value="Da"/> + </section> + <section name="modifications"> + <param name="fixed" value="Carbamidomethyl (C)"/> + <param name="variable" value="Oxidation (M)"/> + <param name="variable_max_per_peptide" value="1"/> + </section> + <section name="peptide"> + <param name="min_size" value="5"/> + <param name="missed_cleavages" value="1"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="cross_linker"> + <param name="residue1" value=""D" "E" "C-term""/> + <param name="residue2" value=""K" "S" "T" "Y" "N-term""/> + <param name="mass" value="-18.010595"/> + <param name="mass_mono_link" value=""/> + <param name="name" value="DMTMM"/> + </section> + <section name="algorithm"> + <param name="number_top_hits" value="1"/> + <param name="deisotope" value="auto"/> + <param name="use_sequence_tags" value="false"/> + <param name="sequence_tag_min_length" value="2"/> + </section> + <section name="ions"> + <param name="b_ions" value="true"/> + <param name="y_ions" value="true"/> + <param name="a_ions" value="false"/> + <param name="x_ions" value="false"/> + <param name="c_ions" value="false"/> + <param name="z_ions" value="false"/> + <param name="neutral_losses" value="true"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_OpenPepXL"> + <test expect_num_outputs="5"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenPepXL_input.mzML"/> + <param name="consensus" value="OpenPepXL_input.consensusXML"/> + <param name="database" value="OpenPepXL_input.fasta"/> + <param name="decoy_string" value="decoy"/> + <param name="decoy_prefix" value="true"/> + <output name="out_idXML" file="OpenPepXL_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <output name="out_mzIdentML" file="OpenPepXL_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/> + <output name="out_xquestxml" file="OpenPepXL_output.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> + <output name="out_xquest_specxml" file="OpenPepXL_output.spec.xml" compare="sim_size" delta="5700" ftype="spec.xml"/> + <section name="precursor"> + <param name="mass_tolerance" value="10.0"/> + <param name="mass_tolerance_unit" value="ppm"/> + <param name="min_charge" value="3"/> + <param name="max_charge" value="7"/> + <param name="corrections" value="2 1 0"/> + </section> + <section name="fragment"> + <param name="mass_tolerance" value="0.2"/> + <param name="mass_tolerance_xlinks" value="0.3"/> + <param name="mass_tolerance_unit" value="Da"/> + </section> + <section name="modifications"> + <param name="fixed" value=""/> + <param name="variable" value=""/> + <param name="variable_max_per_peptide" value="2"/> + </section> + <section name="peptide"> + <param name="min_size" value="5"/> + <param name="missed_cleavages" value="2"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="cross_linker"> + <param name="residue1" value=""K" "N-term""/> + <param name="residue2" value=""K" "N-term""/> + <param name="mass_light" value="138.0680796"/> + <param name="mass_iso_shift" value="12.075321"/> + <param name="mass_mono_link" value="156.07864431 155.094628715"/> + <param name="name" value="DSS"/> + </section> + <section name="algorithm"> + <param name="number_top_hits" value="5"/> + <param name="deisotope" value="auto"/> + </section> + <section name="ions"> + <param name="b_ions" value="true"/> + <param name="y_ions" value="true"/> + <param name="a_ions" value="false"/> + <param name="x_ions" value="false"/> + <param name="c_ions" value="false"/> + <param name="z_ions" value="false"/> + <param name="neutral_losses" value="true"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquestxml_FLAG,out_xquest_specxml_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_OpenSwathAnalyzer"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> + <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> + <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> + <output name="out" file="OpenSwathAnalyzer_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="no_strict" value="false"/> + <param name="min_upper_edge_dist" value="0.0"/> + <section name="model"> + <param name="type" value="linear"/> + <param name="symmetric_regression" value="false"/> + </section> + <section name="algorithm"> + <param name="stop_report_after_feature" value="-1"/> + <param name="rt_extraction_window" value="-1.0"/> + <param name="rt_normalization_factor" value="1.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="stop_after_intensity_ratio" value="0.0001"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="false"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="1.0"/> + <param name="minimal_quality" value="-10000.0"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="15"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="50.0"/> + <param name="use_gauss" value="true"/> + <param name="peak_width" value="40.0"/> + <param name="signal_to_noise" value="1.0"/> + <param name="sn_win_len" value="1000.0"/> + <param name="sn_bin_count" value="30"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="false"/> + <param name="method" value="legacy"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="interpolation_step" value="0.2"/> + <param name="tolerance_stdev_bounding_box" value="3.0"/> + <param name="max_iteration" value="500"/> + <section name="statistics"> + <param name="mean" value="1.0"/> + <param name="variance" value="1.0"/> + </section> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_elution_model_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="false"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="false"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> + <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> + <output name="out" file="OpenSwathAnalyzer_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="no_strict" value="false"/> + <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> + <param name="min_upper_edge_dist" value="0.0"/> + <section name="model"> + <param name="type" value="linear"/> + <param name="symmetric_regression" value="false"/> + </section> + <section name="algorithm"> + <param name="stop_report_after_feature" value="-1"/> + <param name="rt_extraction_window" value="-1.0"/> + <param name="rt_normalization_factor" value="1.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="stop_after_intensity_ratio" value="0.0001"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="false"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="1.0"/> + <param name="minimal_quality" value="-10000.0"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="15"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="50.0"/> + <param name="use_gauss" value="true"/> + <param name="peak_width" value="40.0"/> + <param name="signal_to_noise" value="1.0"/> + <param name="sn_win_len" value="1000.0"/> + <param name="sn_bin_count" value="30"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="false"/> + <param name="method" value="legacy"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="interpolation_step" value="0.2"/> + <param name="tolerance_stdev_bounding_box" value="3.0"/> + <param name="max_iteration" value="500"/> + <section name="statistics"> + <param name="mean" value="1.0"/> + <param name="variance" value="1.0"/> + </section> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_elution_model_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="false"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="false"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> + <param name="tr" value="OpenSwathAnalyzer_mod_input.TraML"/> + <output name="out" file="OpenSwathAnalyzer_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="no_strict" value="false"/> + <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> + <param name="min_upper_edge_dist" value="0.0"/> + <section name="model"> + <param name="type" value="linear"/> + <param name="symmetric_regression" value="false"/> + </section> + <section name="algorithm"> + <param name="stop_report_after_feature" value="-1"/> + <param name="rt_extraction_window" value="-1.0"/> + <param name="rt_normalization_factor" value="1.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="stop_after_intensity_ratio" value="0.0001"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="false"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="1.0"/> + <param name="minimal_quality" value="-10000.0"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="15"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="50.0"/> + <param name="use_gauss" value="true"/> + <param name="peak_width" value="40.0"/> + <param name="signal_to_noise" value="1.0"/> + <param name="sn_win_len" value="1000.0"/> + <param name="sn_bin_count" value="30"/> + <param name="write_sn_log_messages" value="true"/> + <param name="remove_overlapping_peaks" value="false"/> + <param name="method" value="legacy"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="8.0"/> + <param name="dia_byseries_ppm_diff" value="15.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="interpolation_step" value="0.2"/> + <param name="tolerance_stdev_bounding_box" value="3.0"/> + <param name="max_iteration" value="500"/> + <section name="statistics"> + <param name="mean" value="1.0"/> + <param name="variance" value="1.0"/> + </section> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_elution_model_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="false"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="false"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> + <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> + <output name="out" file="OpenSwathAnalyzer_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="no_strict" value="false"/> + <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> + <param name="min_upper_edge_dist" value="0.0"/> + <section name="model"> + <param name="type" value="linear"/> + <param name="symmetric_regression" value="false"/> + </section> + <section name="algorithm"> + <param name="stop_report_after_feature" value="-1"/> + <param name="rt_extraction_window" value="-1.0"/> + <param name="rt_normalization_factor" value="1.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="stop_after_intensity_ratio" value="0.0001"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="false"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="1.0"/> + <param name="minimal_quality" value="-10000.0"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="15"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="50.0"/> + <param name="use_gauss" value="true"/> + <param name="peak_width" value="40.0"/> + <param name="signal_to_noise" value="1.0"/> + <param name="sn_win_len" value="1000.0"/> + <param name="sn_bin_count" value="30"/> + <param name="write_sn_log_messages" value="true"/> + <param name="remove_overlapping_peaks" value="false"/> + <param name="method" value="legacy"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="8.0"/> + <param name="dia_byseries_ppm_diff" value="15.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="interpolation_step" value="0.2"/> + <param name="tolerance_stdev_bounding_box" value="3.0"/> + <param name="max_iteration" value="500"/> + <section name="statistics"> + <param name="mean" value="1.0"/> + <param name="variance" value="1.0"/> + </section> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_elution_model_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="false"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="false"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> + <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> + <output name="out" file="OpenSwathAnalyzer_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="no_strict" value="false"/> + <param name="min_upper_edge_dist" value="0.0"/> + <section name="model"> + <param name="type" value="linear"/> + <param name="symmetric_regression" value="false"/> + </section> + <section name="algorithm"> + <param name="stop_report_after_feature" value="-1"/> + <param name="rt_extraction_window" value="-1.0"/> + <param name="rt_normalization_factor" value="1.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="stop_after_intensity_ratio" value="0.0001"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="original"/> + <param name="recalculate_peaks" value="false"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="1.0"/> + <param name="minimal_quality" value="-10000.0"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="15"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="50.0"/> + <param name="use_gauss" value="true"/> + <param name="peak_width" value="40.0"/> + <param name="signal_to_noise" value="1.0"/> + <param name="sn_win_len" value="1000.0"/> + <param name="sn_bin_count" value="30"/> + <param name="write_sn_log_messages" value="true"/> + <param name="remove_overlapping_peaks" value="false"/> + <param name="method" value="legacy"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="interpolation_step" value="0.2"/> + <param name="tolerance_stdev_bounding_box" value="3.0"/> + <param name="max_iteration" value="500"/> + <section name="statistics"> + <param name="mean" value="1.0"/> + <param name="variance" value="1.0"/> + </section> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_elution_model_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="false"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="false"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> + <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> + <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> + <output name="out" file="OpenSwathAnalyzer_8_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="no_strict" value="false"/> + <param name="min_upper_edge_dist" value="0.0"/> + <section name="model"> + <param name="type" value="linear"/> + <param name="symmetric_regression" value="false"/> + </section> + <section name="algorithm"> + <param name="stop_report_after_feature" value="-1"/> + <param name="rt_extraction_window" value="-1.0"/> + <param name="rt_normalization_factor" value="1.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="stop_after_intensity_ratio" value="0.0001"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="false"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="1.0"/> + <param name="minimal_quality" value="-10000.0"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="15"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="50.0"/> + <param name="use_gauss" value="true"/> + <param name="peak_width" value="40.0"/> + <param name="signal_to_noise" value="1.0"/> + <param name="sn_win_len" value="1000.0"/> + <param name="sn_bin_count" value="30"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="false"/> + <param name="method" value="legacy"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="interpolation_step" value="0.2"/> + <param name="tolerance_stdev_bounding_box" value="3.0"/> + <param name="max_iteration" value="500"/> + <section name="statistics"> + <param name="mean" value="1.0"/> + <param name="variance" value="1.0"/> + </section> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_elution_model_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="true"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="true"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> + <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> + <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> + <output name="out" file="OpenSwathAnalyzer_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="no_strict" value="false"/> + <param name="min_upper_edge_dist" value="0.0"/> + <section name="model"> + <param name="type" value="linear"/> + <param name="symmetric_regression" value="false"/> + </section> + <section name="algorithm"> + <param name="stop_report_after_feature" value="-1"/> + <param name="rt_extraction_window" value="-1.0"/> + <param name="rt_normalization_factor" value="1.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="stop_after_intensity_ratio" value="0.0001"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="false"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="1.0"/> + <param name="minimal_quality" value="-10000.0"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="15"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="50.0"/> + <param name="use_gauss" value="true"/> + <param name="peak_width" value="40.0"/> + <param name="signal_to_noise" value="1.0"/> + <param name="sn_win_len" value="1000.0"/> + <param name="sn_bin_count" value="30"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="false"/> + <param name="method" value="legacy"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="interpolation_step" value="0.2"/> + <param name="tolerance_stdev_bounding_box" value="3.0"/> + <param name="max_iteration" value="500"/> + <section name="statistics"> + <param name="mean" value="1.0"/> + <param name="variance" value="1.0"/> + </section> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_elution_model_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="false"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> + <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> + <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> + <output name="out" file="OpenSwathAnalyzer_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="no_strict" value="false"/> + <param name="min_upper_edge_dist" value="0.0"/> + <section name="model"> + <param name="type" value="linear"/> + <param name="symmetric_regression" value="false"/> + </section> + <section name="algorithm"> + <param name="stop_report_after_feature" value="-1"/> + <param name="rt_extraction_window" value="-1.0"/> + <param name="rt_normalization_factor" value="1.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="stop_after_intensity_ratio" value="0.0001"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="false"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="1.0"/> + <param name="minimal_quality" value="-10000.0"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="15"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="50.0"/> + <param name="use_gauss" value="true"/> + <param name="peak_width" value="40.0"/> + <param name="signal_to_noise" value="1.0"/> + <param name="sn_win_len" value="1000.0"/> + <param name="sn_bin_count" value="30"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="false"/> + <param name="method" value="legacy"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="interpolation_step" value="0.2"/> + <param name="tolerance_stdev_bounding_box" value="3.0"/> + <param name="max_iteration" value="500"/> + <section name="statistics"> + <param name="mean" value="1.0"/> + <param name="variance" value="1.0"/> + </section> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_elution_model_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="true"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="false"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> + <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> + <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> + <output name="out" file="OpenSwathAnalyzer_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="no_strict" value="false"/> + <param name="min_upper_edge_dist" value="0.0"/> + <section name="model"> + <param name="type" value="linear"/> + <param name="symmetric_regression" value="false"/> + </section> + <section name="algorithm"> + <param name="stop_report_after_feature" value="-1"/> + <param name="rt_extraction_window" value="-1.0"/> + <param name="rt_normalization_factor" value="1.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="stop_after_intensity_ratio" value="0.0001"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="false"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="1.0"/> + <param name="minimal_quality" value="-10000.0"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="15"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="50.0"/> + <param name="use_gauss" value="true"/> + <param name="peak_width" value="40.0"/> + <param name="signal_to_noise" value="1.0"/> + <param name="sn_win_len" value="1000.0"/> + <param name="sn_bin_count" value="30"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="false"/> + <param name="method" value="legacy"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="interpolation_step" value="0.2"/> + <param name="tolerance_stdev_bounding_box" value="3.0"/> + <param name="max_iteration" value="500"/> + <section name="statistics"> + <param name="mean" value="1.0"/> + <param name="variance" value="1.0"/> + </section> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_elution_model_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="true"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="false"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="false"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_OpenSwathAssayGenerator"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="max_num_alternative_localizations" value="10000"/> + <param name="disable_identification_ms2_precursors" value="false"/> + <param name="disable_identification_specific_losses" value="false"/> + <param name="enable_identification_unspecific_losses" value="false"/> + <param name="enable_swath_specifity" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathAssayGenerator_input.TraML"/> + <output name="out" file="OpenSwathAssayGenerator_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <param name="min_transitions" value="6"/> + <param name="max_transitions" value="6"/> + <param name="allowed_fragment_types" value="b,y"/> + <param name="allowed_fragment_charges" value="2,3"/> + <param name="enable_detection_specific_losses" value="true"/> + <param name="enable_detection_unspecific_losses" value="false"/> + <param name="precursor_mz_threshold" value="0.025"/> + <param name="precursor_lower_mz_limit" value="400.0"/> + <param name="precursor_upper_mz_limit" value="1200.0"/> + <param name="product_mz_threshold" value="0.025"/> + <param name="product_lower_mz_limit" value="350.0"/> + <param name="product_upper_mz_limit" value="2000.0"/> + <param name="enable_ipf" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="max_num_alternative_localizations" value="10000"/> + <param name="disable_identification_ms2_precursors" value="false"/> + <param name="disable_identification_specific_losses" value="false"/> + <param name="enable_identification_unspecific_losses" value="false"/> + <param name="enable_swath_specifity" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/> + <output name="out" file="OpenSwathAssayGenerator_output_2.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <param name="min_transitions" value="6"/> + <param name="max_transitions" value="6"/> + <param name="allowed_fragment_types" value="b,y"/> + <param name="allowed_fragment_charges" value="1,2,3,4"/> + <param name="enable_detection_specific_losses" value="false"/> + <param name="enable_detection_unspecific_losses" value="false"/> + <param name="precursor_mz_threshold" value="0.025"/> + <param name="precursor_lower_mz_limit" value="400.0"/> + <param name="precursor_upper_mz_limit" value="1200.0"/> + <param name="product_mz_threshold" value="0.025"/> + <param name="product_lower_mz_limit" value="350.0"/> + <param name="product_upper_mz_limit" value="2000.0"/> + <param name="unimod_file" value="OpenSwathAssayGenerator_input_2_unimod.xml"/> + <param name="enable_ipf" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="max_num_alternative_localizations" value="10000"/> + <param name="disable_identification_ms2_precursors" value="false"/> + <param name="disable_identification_specific_losses" value="false"/> + <param name="enable_identification_unspecific_losses" value="false"/> + <param name="enable_swath_specifity" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/> + <output name="out" file="OpenSwathAssayGenerator_output_3.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <param name="min_transitions" value="6"/> + <param name="max_transitions" value="6"/> + <param name="allowed_fragment_types" value="b,y"/> + <param name="allowed_fragment_charges" value="1,2,3,4"/> + <param name="enable_detection_specific_losses" value="false"/> + <param name="enable_detection_unspecific_losses" value="false"/> + <param name="precursor_mz_threshold" value="0.025"/> + <param name="precursor_lower_mz_limit" value="400.0"/> + <param name="precursor_upper_mz_limit" value="1200.0"/> + <param name="product_mz_threshold" value="0.025"/> + <param name="product_lower_mz_limit" value="350.0"/> + <param name="product_upper_mz_limit" value="2000.0"/> + <param name="unimod_file" value="OpenSwathAssayGenerator_input_3_unimod.xml"/> + <param name="enable_ipf" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_OpenSwathChromatogramExtractor"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="extraction_function" value="tophat"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> + <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/> + <output name="out" file="OpenSwathChromatogramExtractor_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="rt_window" value="-1.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_window" value="0.05"/> + <param name="ppm" value="false"/> + <param name="is_swath" value="false"/> + <param name="extract_MS1" value="false"/> + <section name="model"> + <param name="type" value="linear"/> + <param name="symmetric_regression" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="extraction_function" value="tophat"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> + <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/> + <param name="rt_norm" value="OpenSwathChromatogramExtractor_input.trafoXML"/> + <output name="out" file="OpenSwathChromatogramExtractor_output_2.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="rt_window" value="50.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_window" value="0.05"/> + <param name="ppm" value="false"/> + <param name="is_swath" value="false"/> + <param name="extract_MS1" value="false"/> + <section name="model"> + <param name="type" value="linear"/> + <param name="symmetric_regression" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="extraction_function" value="tophat"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> + <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/> + <output name="out" file="OpenSwathChromatogramExtractor_output_3.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="rt_window" value="-1.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_window" value="0.05"/> + <param name="ppm" value="false"/> + <param name="is_swath" value="false"/> + <param name="extract_MS1" value="true"/> + <section name="model"> + <param name="type" value="linear"/> + <param name="symmetric_regression" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="extraction_function" value="tophat"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathChromatogramExtractor_4_input.mzML"/> + <param name="tr" value="OpenSwathChromatogramExtractor_4_input.TraML"/> + <output name="out" file="OpenSwathChromatogramExtractor_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="rt_window" value="-1.0"/> + <param name="ion_mobility_window" value="0.05"/> + <param name="mz_window" value="0.05"/> + <param name="ppm" value="false"/> + <param name="is_swath" value="true"/> + <param name="extract_MS1" value="false"/> + <section name="model"> + <param name="type" value="linear"/> + <param name="symmetric_regression" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="extraction_function" value="tophat"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> + <param name="tr" value="OpenSwathChromatogramExtractor_5_input.TraML"/> + <output name="out" file="OpenSwathChromatogramExtractor_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="rt_window" value="-1.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_window" value="0.05"/> + <param name="ppm" value="false"/> + <param name="is_swath" value="false"/> + <param name="extract_MS1" value="true"/> + <section name="model"> + <param name="type" value="linear"/> + <param name="symmetric_regression" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_OpenSwathConfidenceScoring"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> + <param name="lib" value="OpenSwathFeatureXMLToTSV_input.TraML"/> + <output name="out" file="OpenSwathConfidenceScoring_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="trafo" value="OpenSwathConfidenceScoring_1_input.trafoXML"/> + <param name="decoys" value="1"/> + <param name="transitions" value="2"/> + <section name="GLM"> + <param name="intercept" value="3.87333466"/> + <param name="delta_rt" value="-0.02898629"/> + <param name="dist_int" value="-7.75880768"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_OpenSwathDecoyGenerator"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="min_decoy_fraction" value="0.8"/> + <param name="aim_decoy_fraction" value="1.0"/> + <param name="shuffle_max_attempts" value="30"/> + <param name="shuffle_sequence_identity_threshold" value="0.5"/> + <param name="shift_precursor_mz_shift" value="0.0"/> + <param name="shift_product_mz_shift" value="20.0"/> + <param name="product_mz_threshold" value="0.025"/> + <param name="allowed_fragment_types" value="b,y"/> + <param name="allowed_fragment_charges" value="1,2,3,4"/> + <param name="enable_detection_specific_losses" value="false"/> + <param name="enable_detection_unspecific_losses" value="false"/> + <param name="separate" value="true"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathDecoyGenerator_input.TraML"/> + <output name="out" file="OpenSwathDecoyGenerator_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <param name="method" value="pseudo-reverse"/> + <param name="decoy_tag" value="DECOY_"/> + <param name="switchKR" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="min_decoy_fraction" value="0.8"/> + <param name="aim_decoy_fraction" value="1.0"/> + <param name="shuffle_max_attempts" value="30"/> + <param name="shuffle_sequence_identity_threshold" value="0.5"/> + <param name="shift_precursor_mz_shift" value="0.0"/> + <param name="shift_product_mz_shift" value="20.0"/> + <param name="product_mz_threshold" value="0.8"/> + <param name="allowed_fragment_types" value="b,y"/> + <param name="allowed_fragment_charges" value="1,2,3,4"/> + <param name="enable_detection_specific_losses" value="false"/> + <param name="enable_detection_unspecific_losses" value="false"/> + <param name="separate" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathDecoyGenerator_input_2.TraML"/> + <output name="out" file="OpenSwathDecoyGenerator_output_2.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <param name="method" value="pseudo-reverse"/> + <param name="decoy_tag" value="DECOY_"/> + <param name="switchKR" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="min_decoy_fraction" value="0.8"/> + <param name="aim_decoy_fraction" value="1.0"/> + <param name="shuffle_max_attempts" value="30"/> + <param name="shuffle_sequence_identity_threshold" value="0.5"/> + <param name="shift_precursor_mz_shift" value="0.0"/> + <param name="shift_product_mz_shift" value="20.0"/> + <param name="product_mz_threshold" value="0.025"/> + <param name="allowed_fragment_types" value="b,y"/> + <param name="allowed_fragment_charges" value="1,2,3,4"/> + <param name="enable_detection_specific_losses" value="false"/> + <param name="enable_detection_unspecific_losses" value="false"/> + <param name="separate" value="true"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathDecoyGenerator_input_3.TraML"/> + <output name="out" file="OpenSwathDecoyGenerator_output_3.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <param name="method" value="pseudo-reverse"/> + <param name="decoy_tag" value="DECOY_"/> + <param name="switchKR" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="min_decoy_fraction" value="0.4"/> + <param name="aim_decoy_fraction" value="1.0"/> + <param name="shuffle_max_attempts" value="30"/> + <param name="shuffle_sequence_identity_threshold" value="0.5"/> + <param name="shift_precursor_mz_shift" value="0.0"/> + <param name="shift_product_mz_shift" value="20.0"/> + <param name="product_mz_threshold" value="0.025"/> + <param name="allowed_fragment_types" value="b,y"/> + <param name="allowed_fragment_charges" value="1,2,3,4"/> + <param name="enable_detection_specific_losses" value="true"/> + <param name="enable_detection_unspecific_losses" value="true"/> + <param name="separate" value="true"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathDecoyGenerator_input_4.tsv" ftype="tabular"/> + <output name="out" file="OpenSwathDecoyGenerator_output_4.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <param name="method" value="pseudo-reverse"/> + <param name="decoy_tag" value="DECOY_"/> + <param name="switchKR" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_OpenSwathDIAPreScoring"> +</xml> + <xml name="autotest_OpenSwathFeatureXMLToTSV"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> + <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/> + <output name="out" file="OpenSwathFeatureXMLToTSV_output.short.csv" compare="sim_size" delta="5700" ftype="csv"/> + <param name="short_format" value="true"/> + <param name="best_scoring_peptide" value=""/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> + <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/> + <output name="out" file="OpenSwathFeatureXMLToTSV_output.long.csv" compare="sim_size" delta="5700" ftype="csv"/> + <param name="short_format" value="false"/> + <param name="best_scoring_peptide" value=""/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> + <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/> + <output name="out" file="OpenSwathFeatureXMLToTSV_3_output.short.csv" compare="sim_size" delta="5700" ftype="csv"/> + <param name="short_format" value="true"/> + <param name="best_scoring_peptide" value="main_var_xx_lda_prelim_score"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_OpenSwathFileSplitter"/> + <xml name="autotest_OpenSwathMzMLFileCacher"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="process_lowmemory" value="false"/> + <param name="lowmem_batchsize" value="500"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> + <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzml"/> + <param name="lossy_compression" value="true"/> + <param name="full_meta" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="process_lowmemory" value="false"/> + <param name="lowmem_batchsize" value="500"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/> + <output name="out" file="OpenSwathMzMLFileCacher_2_input.chrom.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzml"/> + <param name="lossy_compression" value="true"/> + <param name="full_meta" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="lossy_mass_accuracy" value="0.0001"/> + <param name="process_lowmemory" value="false"/> + <param name="lowmem_batchsize" value="500"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> + <output name="out" file="OpenSwathMzMLFileCacher_3_input.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/> + <param name="out_type" value="sqmass"/> + <param name="lossy_compression" value="true"/> + <param name="full_meta" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="process_lowmemory" value="false"/> + <param name="lowmem_batchsize" value="500"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathMzMLFileCacher_3_input.tmp.sqMass"/> + <output name="out" file="OpenSwathMzMLFileCacher_3_output.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzml"/> + <param name="lossy_compression" value="true"/> + <param name="full_meta" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="process_lowmemory" value="false"/> + <param name="lowmem_batchsize" value="500"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/> + <output name="out" file="OpenSwathMzMLFileCacher_4_input.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/> + <param name="out_type" value="sqmass"/> + <param name="lossy_compression" value="true"/> + <param name="full_meta" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="process_lowmemory" value="false"/> + <param name="lowmem_batchsize" value="500"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathMzMLFileCacher_4_input.tmp.sqMass"/> + <output name="out" file="OpenSwathMzMLFileCacher_4_output.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzml"/> + <param name="lossy_compression" value="true"/> + <param name="full_meta" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="process_lowmemory" value="true"/> + <param name="lowmem_batchsize" value="500"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> + <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzml"/> + <param name="lossy_compression" value="true"/> + <param name="full_meta" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="process_lowmemory" value="false"/> + <param name="lowmem_batchsize" value="500"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathAnalyzer_2_swathfile.mzML"/> + <output name="out" file="OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp" compare="sim_size" delta="5700"/> + <param name="out_type" value="mzML"/> + <param name="lossy_compression" value="true"/> + <param name="full_meta" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="lossy_mass_accuracy" value="-1.0"/> + <param name="process_lowmemory" value="false"/> + <param name="lowmem_batchsize" value="500"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> + <output name="out" file="OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp" compare="sim_size" delta="5700"/> + <param name="out_type" value="mzML"/> + <param name="lossy_compression" value="true"/> + <param name="full_meta" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="lossy_mass_accuracy" value="0.0001"/> + <param name="process_lowmemory" value="false"/> + <param name="lowmem_batchsize" value="500"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_14.chrom.tmp.sqMass"/> + <output name="out" file="OpenSwathWorkflow_14.chrom.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="out_type" value="mzml"/> + <param name="lossy_compression" value="false"/> + <param name="full_meta" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_OpenSwathRewriteToFeatureXML"> +</xml> + <xml name="autotest_OpenSwathRTNormalizer"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/> + <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/> + <output name="out" file="OpenSwathRTNormalizer_1_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="estimateBestPeptides" value="false"/> + <section name="RTNormalization"> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + </section> + <section name="algorithm"> + <param name="stop_report_after_feature" value="-1"/> + <param name="rt_extraction_window" value="-1.0"/> + <param name="rt_normalization_factor" value="1.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="stop_after_intensity_ratio" value="0.0001"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="false"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="1.0"/> + <param name="minimal_quality" value="-10000.0"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="15"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="50.0"/> + <param name="use_gauss" value="true"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="1.0"/> + <param name="sn_win_len" value="1000.0"/> + <param name="sn_bin_count" value="30"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="false"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="interpolation_step" value="0.2"/> + <param name="tolerance_stdev_bounding_box" value="3.0"/> + <param name="max_iteration" value="500"/> + <section name="statistics"> + <param name="mean" value="1.0"/> + <param name="variance" value="1.0"/> + </section> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_elution_model_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="false"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="false"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <section name="peptideEstimation"> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/> + <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/> + <output name="out" file="OpenSwathRTNormalizer_3_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="estimateBestPeptides" value="true"/> + <section name="RTNormalization"> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + </section> + <section name="algorithm"> + <param name="stop_report_after_feature" value="-1"/> + <param name="rt_extraction_window" value="-1.0"/> + <param name="rt_normalization_factor" value="1.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="stop_after_intensity_ratio" value="0.0001"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="false"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="1.0"/> + <param name="minimal_quality" value="-10000.0"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="15"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="50.0"/> + <param name="use_gauss" value="true"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="1.0"/> + <param name="sn_win_len" value="1000.0"/> + <param name="sn_bin_count" value="30"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="false"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="interpolation_step" value="0.2"/> + <param name="tolerance_stdev_bounding_box" value="3.0"/> + <param name="max_iteration" value="500"/> + <section name="statistics"> + <param name="mean" value="1.0"/> + <param name="variance" value="1.0"/> + </section> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_elution_model_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="false"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="false"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <section name="peptideEstimation"> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="3"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="3"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/> + <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/> + <output name="out" file="OpenSwathRTNormalizer_4_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="estimateBestPeptides" value="false"/> + <section name="RTNormalization"> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + </section> + <section name="algorithm"> + <param name="stop_report_after_feature" value="-1"/> + <param name="rt_extraction_window" value="-1.0"/> + <param name="rt_normalization_factor" value="1.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="stop_after_intensity_ratio" value="0.0001"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="false"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="1.0"/> + <param name="minimal_quality" value="-10000.0"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="15"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="50.0"/> + <param name="use_gauss" value="true"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="1.0"/> + <param name="sn_win_len" value="1000.0"/> + <param name="sn_bin_count" value="30"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="false"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="interpolation_step" value="0.2"/> + <param name="tolerance_stdev_bounding_box" value="3.0"/> + <param name="max_iteration" value="500"/> + <section name="statistics"> + <param name="mean" value="1.0"/> + <param name="variance" value="1.0"/> + </section> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_elution_model_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="false"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="false"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <section name="peptideEstimation"> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_OpenSwathWorkflow"> + <test expect_num_outputs="4"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> + <param name="sort_swath_maps" value="false"/> + <param name="enable_ms1" value="false"/> + <param name="enable_ipf" value="true"/> + <param name="out_chrom_type" value="mzML"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="extra_rt_extraction_window" value="0.0"/> + <param name="mz_extraction_window_unit" value="ppm"/> + <param name="mz_extraction_window_ms1_unit" value="ppm"/> + <param name="use_ms1_ion_mobility" value="true"/> + <param name="matching_window_only" value="false"/> + <param name="irt_mz_extraction_window" value="50.0"/> + <param name="irt_mz_extraction_window_unit" value="ppm"/> + <param name="irt_im_extraction_window" value="-1.0"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="split_file_input" value="false"/> + <param name="use_elution_model_score" value="false"/> + <param name="readOptions" value="normal"/> + <param name="mz_correction_function" value="none"/> + <param name="extraction_function" value="tophat"/> + <param name="batchSize" value="1000"/> + <param name="ms1_isotopes" value="3"/> + <param name="force" value="false"/> + <param name="test" value="false"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> + <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> + <param name="tr_type" value=""/> + <output name="out_features" file="OpenSwathWorkflow_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_chrom" file="OpenSwathWorkflow_1_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <output name="out_qc" file="OpenSwathWorkflow_1_output.json" compare="sim_size" delta="5700" ftype="json"/> + <param name="sonar" value="false"/> + <param name="rt_extraction_window" value="600.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_extraction_window" value="50.0"/> + <param name="mz_extraction_window_ms1" value="50.0"/> + <param name="im_extraction_window_ms1" value="-1.0"/> + <section name="Debugging"/> + <section name="Calibration"> + <param name="ms1_im_calibration" value="false"/> + <param name="im_correction_function" value="linear"/> + <param name="debug_im_file" value=""/> + <param name="debug_mz_file" value=""/> + </section> + <section name="Library"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <section name="RTNormalization"> + <param name="alignmentMethod" value="linear"/> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + <param name="estimateBestPeptides" value="false"/> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + <section name="lowess"> + <param name="span" value="0.05"/> + </section> + <section name="b_spline"> + <param name="num_nodes" value="5"/> + </section> + </section> + <section name="Scoring"> + <param name="stop_report_after_feature" value="5"/> + <param name="rt_normalization_factor" value="100.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="true"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="0.75"/> + <param name="minimal_quality" value="-1.5"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="11"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="30.0"/> + <param name="use_gauss" value="false"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="0.1"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="max_iteration" value="10"/> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="true"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,out_qc_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="rt_norm" value="OpenSwathWorkflow_2_input.trafoXML"/> + <param name="sort_swath_maps" value="false"/> + <param name="enable_ms1" value="false"/> + <param name="enable_ipf" value="true"/> + <param name="out_chrom_type" value="mzML"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="extra_rt_extraction_window" value="0.0"/> + <param name="mz_extraction_window_unit" value="ppm"/> + <param name="mz_extraction_window_ms1_unit" value="ppm"/> + <param name="use_ms1_ion_mobility" value="true"/> + <param name="matching_window_only" value="false"/> + <param name="irt_mz_extraction_window" value="50.0"/> + <param name="irt_mz_extraction_window_unit" value="ppm"/> + <param name="irt_im_extraction_window" value="-1.0"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="split_file_input" value="false"/> + <param name="use_elution_model_score" value="false"/> + <param name="readOptions" value="normal"/> + <param name="mz_correction_function" value="none"/> + <param name="extraction_function" value="tophat"/> + <param name="batchSize" value="1000"/> + <param name="ms1_isotopes" value="3"/> + <param name="force" value="false"/> + <param name="test" value="false"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_2_input.mzXML"/> + <param name="tr" value="OpenSwathWorkflow_2_input.TraML"/> + <param name="tr_type" value=""/> + <output name="out_features" file="OpenSwathWorkflow_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_chrom" file="OpenSwathWorkflow_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="sonar" value="false"/> + <param name="rt_extraction_window" value="600.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_extraction_window" value="50.0"/> + <param name="mz_extraction_window_ms1" value="50.0"/> + <param name="im_extraction_window_ms1" value="-1.0"/> + <section name="Debugging"/> + <section name="Calibration"> + <param name="ms1_im_calibration" value="false"/> + <param name="im_correction_function" value="linear"/> + <param name="debug_im_file" value=""/> + <param name="debug_mz_file" value=""/> + </section> + <section name="Library"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <section name="RTNormalization"> + <param name="alignmentMethod" value="linear"/> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + <param name="estimateBestPeptides" value="false"/> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + <section name="lowess"> + <param name="span" value="0.05"/> + </section> + <section name="b_spline"> + <param name="num_nodes" value="5"/> + </section> + </section> + <section name="Scoring"> + <param name="stop_report_after_feature" value="5"/> + <param name="rt_normalization_factor" value="100.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="true"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="0.75"/> + <param name="minimal_quality" value="-1.5"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="11"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="30.0"/> + <param name="use_gauss" value="false"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="0.1"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="max_iteration" value="10"/> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="true"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> + <param name="sort_swath_maps" value="false"/> + <param name="enable_ms1" value="true"/> + <param name="enable_ipf" value="true"/> + <param name="out_chrom_type" value="mzML"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="extra_rt_extraction_window" value="0.0"/> + <param name="mz_extraction_window_unit" value="ppm"/> + <param name="mz_extraction_window_ms1_unit" value="ppm"/> + <param name="use_ms1_ion_mobility" value="true"/> + <param name="matching_window_only" value="false"/> + <param name="irt_mz_extraction_window" value="50.0"/> + <param name="irt_mz_extraction_window_unit" value="ppm"/> + <param name="irt_im_extraction_window" value="-1.0"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="split_file_input" value="false"/> + <param name="use_elution_model_score" value="false"/> + <param name="readOptions" value="normal"/> + <param name="mz_correction_function" value="none"/> + <param name="extraction_function" value="tophat"/> + <param name="batchSize" value="1000"/> + <param name="ms1_isotopes" value="3"/> + <param name="force" value="false"/> + <param name="test" value="false"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> + <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> + <param name="tr_type" value=""/> + <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="sonar" value="false"/> + <param name="rt_extraction_window" value="600.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_extraction_window" value="50.0"/> + <param name="mz_extraction_window_ms1" value="50.0"/> + <param name="im_extraction_window_ms1" value="-1.0"/> + <section name="Debugging"/> + <section name="Calibration"> + <param name="ms1_im_calibration" value="false"/> + <param name="im_correction_function" value="linear"/> + <param name="debug_im_file" value=""/> + <param name="debug_mz_file" value=""/> + </section> + <section name="Library"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <section name="RTNormalization"> + <param name="alignmentMethod" value="linear"/> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + <param name="estimateBestPeptides" value="false"/> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + <section name="lowess"> + <param name="span" value="0.05"/> + </section> + <section name="b_spline"> + <param name="num_nodes" value="5"/> + </section> + </section> + <section name="Scoring"> + <param name="stop_report_after_feature" value="5"/> + <param name="rt_normalization_factor" value="100.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="true"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="0.75"/> + <param name="minimal_quality" value="-1.5"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="11"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="30.0"/> + <param name="use_gauss" value="false"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="0.1"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="max_iteration" value="10"/> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="true"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> + <param name="sort_swath_maps" value="false"/> + <param name="enable_ms1" value="true"/> + <param name="enable_ipf" value="true"/> + <param name="out_chrom_type" value="mzML"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="extra_rt_extraction_window" value="0.0"/> + <param name="mz_extraction_window_unit" value="ppm"/> + <param name="mz_extraction_window_ms1_unit" value="ppm"/> + <param name="use_ms1_ion_mobility" value="true"/> + <param name="matching_window_only" value="false"/> + <param name="irt_mz_extraction_window" value="50.0"/> + <param name="irt_mz_extraction_window_unit" value="ppm"/> + <param name="irt_im_extraction_window" value="-1.0"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="split_file_input" value="false"/> + <param name="use_elution_model_score" value="false"/> + <param name="readOptions" value="normal"/> + <param name="mz_correction_function" value="none"/> + <param name="extraction_function" value="tophat"/> + <param name="batchSize" value="1000"/> + <param name="ms1_isotopes" value="3"/> + <param name="force" value="false"/> + <param name="test" value="false"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> + <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> + <param name="tr_type" value=""/> + <output name="out_tsv" file="OpenSwathWorkflow_4.tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/> + <output name="out_chrom" file="OpenSwathWorkflow_4.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="sonar" value="false"/> + <param name="rt_extraction_window" value="600.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_extraction_window" value="50.0"/> + <param name="mz_extraction_window_ms1" value="50.0"/> + <param name="im_extraction_window_ms1" value="-1.0"/> + <section name="Debugging"/> + <section name="Calibration"> + <param name="ms1_im_calibration" value="false"/> + <param name="im_correction_function" value="linear"/> + <param name="debug_im_file" value=""/> + <param name="debug_mz_file" value=""/> + </section> + <section name="Library"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <section name="RTNormalization"> + <param name="alignmentMethod" value="linear"/> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + <param name="estimateBestPeptides" value="false"/> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + <section name="lowess"> + <param name="span" value="0.05"/> + </section> + <section name="b_spline"> + <param name="num_nodes" value="5"/> + </section> + </section> + <section name="Scoring"> + <param name="stop_report_after_feature" value="5"/> + <param name="rt_normalization_factor" value="100.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="true"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="0.75"/> + <param name="minimal_quality" value="-1.5"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="11"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="30.0"/> + <param name="use_gauss" value="false"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="0.1"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="max_iteration" value="10"/> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="true"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG,out_chrom_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> + <param name="sort_swath_maps" value="false"/> + <param name="enable_ms1" value="true"/> + <param name="enable_ipf" value="true"/> + <param name="out_chrom_type" value="mzML"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="extra_rt_extraction_window" value="0.0"/> + <param name="mz_extraction_window_unit" value="ppm"/> + <param name="mz_extraction_window_ms1_unit" value="ppm"/> + <param name="use_ms1_ion_mobility" value="true"/> + <param name="matching_window_only" value="false"/> + <param name="irt_mz_extraction_window" value="50.0"/> + <param name="irt_mz_extraction_window_unit" value="ppm"/> + <param name="irt_im_extraction_window" value="-1.0"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="split_file_input" value="false"/> + <param name="use_elution_model_score" value="false"/> + <param name="readOptions" value="cache"/> + <param name="mz_correction_function" value="none"/> + <param name="extraction_function" value="tophat"/> + <param name="batchSize" value="1000"/> + <param name="ms1_isotopes" value="3"/> + <param name="force" value="false"/> + <param name="test" value="false"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> + <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> + <param name="tr_type" value=""/> + <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="sonar" value="false"/> + <param name="rt_extraction_window" value="600.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_extraction_window" value="50.0"/> + <param name="mz_extraction_window_ms1" value="50.0"/> + <param name="im_extraction_window_ms1" value="-1.0"/> + <section name="Debugging"/> + <section name="Calibration"> + <param name="ms1_im_calibration" value="false"/> + <param name="im_correction_function" value="linear"/> + <param name="debug_im_file" value=""/> + <param name="debug_mz_file" value=""/> + </section> + <section name="Library"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <section name="RTNormalization"> + <param name="alignmentMethod" value="linear"/> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + <param name="estimateBestPeptides" value="false"/> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + <section name="lowess"> + <param name="span" value="0.05"/> + </section> + <section name="b_spline"> + <param name="num_nodes" value="5"/> + </section> + </section> + <section name="Scoring"> + <param name="stop_report_after_feature" value="5"/> + <param name="rt_normalization_factor" value="100.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="true"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="0.75"/> + <param name="minimal_quality" value="-1.5"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="11"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="30.0"/> + <param name="use_gauss" value="false"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="0.1"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="max_iteration" value="10"/> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="true"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> + <param name="sort_swath_maps" value="false"/> + <param name="enable_ms1" value="true"/> + <param name="enable_ipf" value="true"/> + <param name="out_chrom_type" value="mzML"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="extra_rt_extraction_window" value="0.0"/> + <param name="mz_extraction_window_unit" value="ppm"/> + <param name="mz_extraction_window_ms1_unit" value="ppm"/> + <param name="use_ms1_ion_mobility" value="true"/> + <param name="matching_window_only" value="false"/> + <param name="irt_mz_extraction_window" value="50.0"/> + <param name="irt_mz_extraction_window_unit" value="ppm"/> + <param name="irt_im_extraction_window" value="-1.0"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="split_file_input" value="false"/> + <param name="use_elution_model_score" value="false"/> + <param name="readOptions" value="cacheWorkingInMemory"/> + <param name="mz_correction_function" value="none"/> + <param name="extraction_function" value="tophat"/> + <param name="batchSize" value="1000"/> + <param name="ms1_isotopes" value="3"/> + <param name="force" value="false"/> + <param name="test" value="false"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> + <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> + <param name="tr_type" value=""/> + <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="sonar" value="false"/> + <param name="rt_extraction_window" value="600.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_extraction_window" value="50.0"/> + <param name="mz_extraction_window_ms1" value="50.0"/> + <param name="im_extraction_window_ms1" value="-1.0"/> + <section name="Debugging"/> + <section name="Calibration"> + <param name="ms1_im_calibration" value="false"/> + <param name="im_correction_function" value="linear"/> + <param name="debug_im_file" value=""/> + <param name="debug_mz_file" value=""/> + </section> + <section name="Library"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <section name="RTNormalization"> + <param name="alignmentMethod" value="linear"/> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + <param name="estimateBestPeptides" value="false"/> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + <section name="lowess"> + <param name="span" value="0.05"/> + </section> + <section name="b_spline"> + <param name="num_nodes" value="5"/> + </section> + </section> + <section name="Scoring"> + <param name="stop_report_after_feature" value="5"/> + <param name="rt_normalization_factor" value="100.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="true"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="0.75"/> + <param name="minimal_quality" value="-1.5"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="11"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="30.0"/> + <param name="use_gauss" value="false"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="0.1"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="max_iteration" value="10"/> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="true"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> + <param name="sort_swath_maps" value="false"/> + <param name="enable_ms1" value="true"/> + <param name="enable_ipf" value="true"/> + <param name="out_chrom_type" value="mzML"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="extra_rt_extraction_window" value="0.0"/> + <param name="mz_extraction_window_unit" value="ppm"/> + <param name="mz_extraction_window_ms1_unit" value="ppm"/> + <param name="use_ms1_ion_mobility" value="true"/> + <param name="matching_window_only" value="false"/> + <param name="irt_mz_extraction_window" value="50.0"/> + <param name="irt_mz_extraction_window_unit" value="ppm"/> + <param name="irt_im_extraction_window" value="-1.0"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="split_file_input" value="false"/> + <param name="use_elution_model_score" value="false"/> + <param name="readOptions" value="normal"/> + <param name="mz_correction_function" value="none"/> + <param name="extraction_function" value="tophat"/> + <param name="batchSize" value="1000"/> + <param name="ms1_isotopes" value="3"/> + <param name="force" value="false"/> + <param name="test" value="false"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> + <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> + <param name="tr_type" value=""/> + <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/> + <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="sonar" value="false"/> + <param name="rt_extraction_window" value="600.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_extraction_window" value="50.0"/> + <param name="mz_extraction_window_ms1" value="50.0"/> + <param name="im_extraction_window_ms1" value="-1.0"/> + <section name="Debugging"/> + <section name="Calibration"> + <param name="ms1_im_calibration" value="false"/> + <param name="im_correction_function" value="linear"/> + <param name="debug_im_file" value=""/> + <param name="debug_mz_file" value=""/> + </section> + <section name="Library"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <section name="RTNormalization"> + <param name="alignmentMethod" value="linear"/> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + <param name="estimateBestPeptides" value="false"/> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + <section name="lowess"> + <param name="span" value="0.05"/> + </section> + <section name="b_spline"> + <param name="num_nodes" value="5"/> + </section> + </section> + <section name="Scoring"> + <param name="stop_report_after_feature" value="5"/> + <param name="rt_normalization_factor" value="100.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="true"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="0.75"/> + <param name="minimal_quality" value="-1.5"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="11"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="30.0"/> + <param name="use_gauss" value="false"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="0.1"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="max_iteration" value="10"/> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="true"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> + <param name="sort_swath_maps" value="false"/> + <param name="enable_ms1" value="true"/> + <param name="enable_ipf" value="true"/> + <param name="out_chrom_type" value="mzML"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="extra_rt_extraction_window" value="0.0"/> + <param name="mz_extraction_window_unit" value="ppm"/> + <param name="mz_extraction_window_ms1_unit" value="ppm"/> + <param name="use_ms1_ion_mobility" value="true"/> + <param name="matching_window_only" value="false"/> + <param name="irt_mz_extraction_window" value="50.0"/> + <param name="irt_mz_extraction_window_unit" value="ppm"/> + <param name="irt_im_extraction_window" value="-1.0"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="split_file_input" value="false"/> + <param name="use_elution_model_score" value="false"/> + <param name="readOptions" value="normal"/> + <param name="mz_correction_function" value="none"/> + <param name="extraction_function" value="tophat"/> + <param name="batchSize" value="1000"/> + <param name="ms1_isotopes" value="3"/> + <param name="force" value="true"/> + <param name="test" value="false"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> + <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> + <param name="tr_type" value=""/> + <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/> + <output name="out_features" file="OpenSwathWorkflow_10.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_chrom" file="OpenSwathWorkflow_10.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="sonar" value="false"/> + <param name="rt_extraction_window" value="600.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_extraction_window" value="50.0"/> + <param name="mz_extraction_window_ms1" value="50.0"/> + <param name="im_extraction_window_ms1" value="-1.0"/> + <section name="Debugging"/> + <section name="Calibration"> + <param name="ms1_im_calibration" value="false"/> + <param name="im_correction_function" value="linear"/> + <param name="debug_im_file" value=""/> + <param name="debug_mz_file" value=""/> + </section> + <section name="Library"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <section name="RTNormalization"> + <param name="alignmentMethod" value="linear"/> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + <param name="estimateBestPeptides" value="false"/> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + <section name="lowess"> + <param name="span" value="0.05"/> + </section> + <section name="b_spline"> + <param name="num_nodes" value="5"/> + </section> + </section> + <section name="Scoring"> + <param name="stop_report_after_feature" value="5"/> + <param name="rt_normalization_factor" value="100.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="true"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="0.75"/> + <param name="minimal_quality" value="-1.5"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="11"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="30.0"/> + <param name="use_gauss" value="false"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="0.1"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="max_iteration" value="10"/> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="true"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="sort_swath_maps" value="false"/> + <param name="enable_ms1" value="false"/> + <param name="enable_ipf" value="true"/> + <param name="out_chrom_type" value="mzML"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="extra_rt_extraction_window" value="0.0"/> + <param name="mz_extraction_window_unit" value="ppm"/> + <param name="mz_extraction_window_ms1_unit" value="ppm"/> + <param name="use_ms1_ion_mobility" value="true"/> + <param name="matching_window_only" value="false"/> + <param name="irt_mz_extraction_window" value="550.0"/> + <param name="irt_mz_extraction_window_unit" value="ppm"/> + <param name="irt_im_extraction_window" value="-1.0"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="split_file_input" value="false"/> + <param name="use_elution_model_score" value="false"/> + <param name="readOptions" value="normal"/> + <param name="mz_correction_function" value="quadratic_regression_delta_ppm"/> + <param name="extraction_function" value="tophat"/> + <param name="batchSize" value="1000"/> + <param name="ms1_isotopes" value="3"/> + <param name="force" value="false"/> + <param name="test" value="false"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_11_input.mzML"/> + <param name="tr" value="OpenSwathWorkflow_11_input_2.TraML"/> + <param name="tr_type" value=""/> + <param name="tr_irt" value="OpenSwathWorkflow_11_input.TraML"/> + <output name="out_features" file="OpenSwathWorkflow_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_chrom" file="OpenSwathWorkflow_11_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="sonar" value="true"/> + <param name="rt_extraction_window" value="-1.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_extraction_window" value="0.2"/> + <param name="mz_extraction_window_ms1" value="50.0"/> + <param name="im_extraction_window_ms1" value="-1.0"/> + <section name="Debugging"/> + <section name="Calibration"> + <param name="ms1_im_calibration" value="false"/> + <param name="im_correction_function" value="linear"/> + <param name="debug_im_file" value=""/> + <param name="debug_mz_file" value=""/> + </section> + <section name="Library"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <section name="RTNormalization"> + <param name="alignmentMethod" value="linear"/> + <param name="outlierMethod" value="none"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + <param name="estimateBestPeptides" value="false"/> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + <section name="lowess"> + <param name="span" value="0.05"/> + </section> + <section name="b_spline"> + <param name="num_nodes" value="5"/> + </section> + </section> + <section name="Scoring"> + <param name="stop_report_after_feature" value="5"/> + <param name="rt_normalization_factor" value="100.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="true"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="0.75"/> + <param name="minimal_quality" value="-1.5"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="11"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="30.0"/> + <param name="use_gauss" value="false"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="0.1"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="max_iteration" value="10"/> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="true"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="true"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> + <param name="sort_swath_maps" value="false"/> + <param name="enable_ms1" value="true"/> + <param name="enable_ipf" value="true"/> + <param name="out_chrom_type" value="mzML"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="extra_rt_extraction_window" value="0.0"/> + <param name="mz_extraction_window_unit" value="ppm"/> + <param name="mz_extraction_window_ms1_unit" value="ppm"/> + <param name="use_ms1_ion_mobility" value="true"/> + <param name="matching_window_only" value="false"/> + <param name="irt_mz_extraction_window" value="50.0"/> + <param name="irt_mz_extraction_window_unit" value="ppm"/> + <param name="irt_im_extraction_window" value="-1.0"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="split_file_input" value="false"/> + <param name="use_elution_model_score" value="false"/> + <param name="readOptions" value="normal"/> + <param name="mz_correction_function" value="none"/> + <param name="extraction_function" value="tophat"/> + <param name="batchSize" value="1000"/> + <param name="ms1_isotopes" value="3"/> + <param name="force" value="false"/> + <param name="test" value="false"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> + <param name="tr" value="OpenSwathWorkflow_13_input.pqp.tmp"/> + <param name="tr_type" value="pqp"/> + <output name="out_osw" file="OpenSwathWorkflow_13.osw" compare="sim_size" delta="5700" ftype="osw"/> + <output name="out_chrom" file="OpenSwathWorkflow_13_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="sonar" value="false"/> + <param name="rt_extraction_window" value="600.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_extraction_window" value="50.0"/> + <param name="mz_extraction_window_ms1" value="50.0"/> + <param name="im_extraction_window_ms1" value="-1.0"/> + <section name="Debugging"/> + <section name="Calibration"> + <param name="ms1_im_calibration" value="false"/> + <param name="im_correction_function" value="linear"/> + <param name="debug_im_file" value=""/> + <param name="debug_mz_file" value=""/> + </section> + <section name="Library"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <section name="RTNormalization"> + <param name="alignmentMethod" value="linear"/> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + <param name="estimateBestPeptides" value="false"/> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + <section name="lowess"> + <param name="span" value="0.05"/> + </section> + <section name="b_spline"> + <param name="num_nodes" value="5"/> + </section> + </section> + <section name="Scoring"> + <param name="stop_report_after_feature" value="5"/> + <param name="rt_normalization_factor" value="100.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="true"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="0.75"/> + <param name="minimal_quality" value="-1.5"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="11"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="30.0"/> + <param name="use_gauss" value="false"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="0.1"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="max_iteration" value="10"/> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="true"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> + <param name="sort_swath_maps" value="false"/> + <param name="enable_ms1" value="true"/> + <param name="enable_ipf" value="true"/> + <param name="out_chrom_type" value="sqMass"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="extra_rt_extraction_window" value="0.0"/> + <param name="mz_extraction_window_unit" value="ppm"/> + <param name="mz_extraction_window_ms1_unit" value="ppm"/> + <param name="use_ms1_ion_mobility" value="true"/> + <param name="matching_window_only" value="false"/> + <param name="irt_mz_extraction_window" value="50.0"/> + <param name="irt_mz_extraction_window_unit" value="ppm"/> + <param name="irt_im_extraction_window" value="-1.0"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="split_file_input" value="false"/> + <param name="use_elution_model_score" value="false"/> + <param name="readOptions" value="normal"/> + <param name="mz_correction_function" value="none"/> + <param name="extraction_function" value="tophat"/> + <param name="batchSize" value="1000"/> + <param name="ms1_isotopes" value="3"/> + <param name="force" value="false"/> + <param name="test" value="false"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> + <param name="tr" value="OpenSwathWorkflow_14_input.pqp.tmp"/> + <param name="tr_type" value="pqp"/> + <output name="out_osw" file="OpenSwathWorkflow_14.osw" compare="sim_size" delta="5700" ftype="osw"/> + <output name="out_chrom" file="OpenSwathWorkflow_14.chrom.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/> + <param name="sonar" value="false"/> + <param name="rt_extraction_window" value="600.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_extraction_window" value="50.0"/> + <param name="mz_extraction_window_ms1" value="50.0"/> + <param name="im_extraction_window_ms1" value="-1.0"/> + <section name="Debugging"/> + <section name="Calibration"> + <param name="ms1_im_calibration" value="false"/> + <param name="im_correction_function" value="linear"/> + <param name="debug_im_file" value=""/> + <param name="debug_mz_file" value=""/> + </section> + <section name="Library"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <section name="RTNormalization"> + <param name="alignmentMethod" value="linear"/> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + <param name="estimateBestPeptides" value="false"/> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + <section name="lowess"> + <param name="span" value="0.05"/> + </section> + <section name="b_spline"> + <param name="num_nodes" value="5"/> + </section> + </section> + <section name="Scoring"> + <param name="stop_report_after_feature" value="5"/> + <param name="rt_normalization_factor" value="100.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="true"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="0.75"/> + <param name="minimal_quality" value="-1.5"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="11"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="30.0"/> + <param name="use_gauss" value="false"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="0.1"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="max_iteration" value="10"/> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="true"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> + <param name="sort_swath_maps" value="false"/> + <param name="enable_ms1" value="true"/> + <param name="enable_ipf" value="true"/> + <param name="out_chrom_type" value="mzML"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="extra_rt_extraction_window" value="0.0"/> + <param name="mz_extraction_window_unit" value="Th"/> + <param name="mz_extraction_window_ms1_unit" value="ppm"/> + <param name="use_ms1_ion_mobility" value="true"/> + <param name="matching_window_only" value="false"/> + <param name="irt_mz_extraction_window" value="50.0"/> + <param name="irt_mz_extraction_window_unit" value="ppm"/> + <param name="irt_im_extraction_window" value="-1.0"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="split_file_input" value="false"/> + <param name="use_elution_model_score" value="false"/> + <param name="readOptions" value="normal"/> + <param name="mz_correction_function" value="none"/> + <param name="extraction_function" value="tophat"/> + <param name="batchSize" value="1000"/> + <param name="ms1_isotopes" value="2"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_15_input.mzML"/> + <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> + <param name="tr_type" value=""/> + <output name="out_features" file="OpenSwathWorkflow_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_chrom" file="OpenSwathWorkflow_15_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="sonar" value="false"/> + <param name="rt_extraction_window" value="600.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_extraction_window" value="0.05"/> + <param name="mz_extraction_window_ms1" value="50.0"/> + <param name="im_extraction_window_ms1" value="-1.0"/> + <section name="Debugging"/> + <section name="Calibration"> + <param name="ms1_im_calibration" value="false"/> + <param name="im_correction_function" value="linear"/> + <param name="debug_im_file" value=""/> + <param name="debug_mz_file" value=""/> + </section> + <section name="Library"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <section name="RTNormalization"> + <param name="alignmentMethod" value="linear"/> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + <param name="estimateBestPeptides" value="false"/> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + <section name="lowess"> + <param name="span" value="0.05"/> + </section> + <section name="b_spline"> + <param name="num_nodes" value="5"/> + </section> + </section> + <section name="Scoring"> + <param name="stop_report_after_feature" value="5"/> + <param name="rt_normalization_factor" value="100.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="true"/> + <param name="use_precursors" value="true"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="0.75"/> + <param name="minimal_quality" value="-1.5"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="11"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="30.0"/> + <param name="use_gauss" value="false"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="0.1"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="max_iteration" value="10"/> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="false"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="false"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> + <param name="sort_swath_maps" value="false"/> + <param name="enable_ms1" value="true"/> + <param name="enable_ipf" value="true"/> + <param name="out_chrom_type" value="mzML"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="extra_rt_extraction_window" value="0.0"/> + <param name="mz_extraction_window_unit" value="ppm"/> + <param name="mz_extraction_window_ms1_unit" value="ppm"/> + <param name="use_ms1_ion_mobility" value="true"/> + <param name="matching_window_only" value="false"/> + <param name="irt_mz_extraction_window" value="50.0"/> + <param name="irt_mz_extraction_window_unit" value="ppm"/> + <param name="irt_im_extraction_window" value="-1.0"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="split_file_input" value="false"/> + <param name="use_elution_model_score" value="false"/> + <param name="readOptions" value="workingInMemory"/> + <param name="mz_correction_function" value="none"/> + <param name="extraction_function" value="tophat"/> + <param name="batchSize" value="1000"/> + <param name="ms1_isotopes" value="2"/> + <param name="force" value="false"/> + <param name="test" value="false"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_16_input.sqMass"/> + <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> + <param name="tr_type" value=""/> + <output name="out_features" file="OpenSwathWorkflow_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_chrom" file="OpenSwathWorkflow_16_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="sonar" value="false"/> + <param name="rt_extraction_window" value="600.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_extraction_window" value="50.0"/> + <param name="mz_extraction_window_ms1" value="50.0"/> + <param name="im_extraction_window_ms1" value="-1.0"/> + <section name="Debugging"/> + <section name="Calibration"> + <param name="ms1_im_calibration" value="false"/> + <param name="im_correction_function" value="linear"/> + <param name="debug_im_file" value=""/> + <param name="debug_mz_file" value=""/> + </section> + <section name="Library"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <section name="RTNormalization"> + <param name="alignmentMethod" value="linear"/> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + <param name="estimateBestPeptides" value="false"/> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + <section name="lowess"> + <param name="span" value="0.05"/> + </section> + <section name="b_spline"> + <param name="num_nodes" value="5"/> + </section> + </section> + <section name="Scoring"> + <param name="stop_report_after_feature" value="5"/> + <param name="rt_normalization_factor" value="100.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="true"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="0.75"/> + <param name="minimal_quality" value="-1.5"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="11"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="30.0"/> + <param name="use_gauss" value="false"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="0.1"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="max_iteration" value="10"/> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="true"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="sort_swath_maps" value="false"/> + <param name="enable_ms1" value="true"/> + <param name="enable_ipf" value="true"/> + <param name="out_chrom_type" value="mzML"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="extra_rt_extraction_window" value="0.0"/> + <param name="mz_extraction_window_unit" value="ppm"/> + <param name="mz_extraction_window_ms1_unit" value="ppm"/> + <param name="use_ms1_ion_mobility" value="false"/> + <param name="matching_window_only" value="false"/> + <param name="irt_mz_extraction_window" value="50.0"/> + <param name="irt_mz_extraction_window_unit" value="ppm"/> + <param name="irt_im_extraction_window" value="-1.0"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="split_file_input" value="false"/> + <param name="use_elution_model_score" value="false"/> + <param name="readOptions" value="workingInMemory"/> + <param name="mz_correction_function" value="none"/> + <param name="extraction_function" value="tophat"/> + <param name="batchSize" value="1000"/> + <param name="ms1_isotopes" value="3"/> + <param name="force" value="false"/> + <param name="test" value="false"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> + <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/> + <param name="tr_type" value=""/> + <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="sonar" value="false"/> + <param name="rt_extraction_window" value="600.0"/> + <param name="ion_mobility_window" value="0.05"/> + <param name="mz_extraction_window" value="50.0"/> + <param name="mz_extraction_window_ms1" value="50.0"/> + <param name="im_extraction_window_ms1" value="-1.0"/> + <section name="Debugging"/> + <section name="Calibration"> + <param name="ms1_im_calibration" value="false"/> + <param name="im_correction_function" value="linear"/> + <param name="debug_im_file" value=""/> + <param name="debug_mz_file" value=""/> + </section> + <section name="Library"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <section name="RTNormalization"> + <param name="alignmentMethod" value="linear"/> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + <param name="estimateBestPeptides" value="false"/> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + <section name="lowess"> + <param name="span" value="0.05"/> + </section> + <section name="b_spline"> + <param name="num_nodes" value="5"/> + </section> + </section> + <section name="Scoring"> + <param name="stop_report_after_feature" value="5"/> + <param name="rt_normalization_factor" value="100.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="true"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="0.75"/> + <param name="minimal_quality" value="-1.5"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="11"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="30.0"/> + <param name="use_gauss" value="false"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="0.1"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="max_iteration" value="10"/> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="true"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="true"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="sort_swath_maps" value="false"/> + <param name="enable_ms1" value="true"/> + <param name="enable_ipf" value="true"/> + <param name="out_chrom_type" value="mzML"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="extra_rt_extraction_window" value="0.0"/> + <param name="mz_extraction_window_unit" value="ppm"/> + <param name="mz_extraction_window_ms1_unit" value="ppm"/> + <param name="use_ms1_ion_mobility" value="false"/> + <param name="matching_window_only" value="false"/> + <param name="irt_mz_extraction_window" value="50.0"/> + <param name="irt_mz_extraction_window_unit" value="ppm"/> + <param name="irt_im_extraction_window" value="-1.0"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="split_file_input" value="false"/> + <param name="use_elution_model_score" value="false"/> + <param name="readOptions" value="cache"/> + <param name="mz_correction_function" value="none"/> + <param name="extraction_function" value="tophat"/> + <param name="batchSize" value="1000"/> + <param name="ms1_isotopes" value="3"/> + <param name="force" value="false"/> + <param name="test" value="false"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> + <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/> + <param name="tr_type" value=""/> + <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="sonar" value="false"/> + <param name="rt_extraction_window" value="600.0"/> + <param name="ion_mobility_window" value="0.05"/> + <param name="mz_extraction_window" value="50.0"/> + <param name="mz_extraction_window_ms1" value="50.0"/> + <param name="im_extraction_window_ms1" value="-1.0"/> + <section name="Debugging"/> + <section name="Calibration"> + <param name="ms1_im_calibration" value="false"/> + <param name="im_correction_function" value="linear"/> + <param name="debug_im_file" value=""/> + <param name="debug_mz_file" value=""/> + </section> + <section name="Library"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <section name="RTNormalization"> + <param name="alignmentMethod" value="linear"/> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + <param name="estimateBestPeptides" value="false"/> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + <section name="lowess"> + <param name="span" value="0.05"/> + </section> + <section name="b_spline"> + <param name="num_nodes" value="5"/> + </section> + </section> + <section name="Scoring"> + <param name="stop_report_after_feature" value="5"/> + <param name="rt_normalization_factor" value="100.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="true"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="0.75"/> + <param name="minimal_quality" value="-1.5"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="11"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="30.0"/> + <param name="use_gauss" value="false"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="0.1"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="max_iteration" value="10"/> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="true"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="true"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="sort_swath_maps" value="false"/> + <param name="enable_ms1" value="true"/> + <param name="enable_ipf" value="true"/> + <param name="out_chrom_type" value="mzML"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="extra_rt_extraction_window" value="0.0"/> + <param name="mz_extraction_window_unit" value="ppm"/> + <param name="mz_extraction_window_ms1_unit" value="ppm"/> + <param name="use_ms1_ion_mobility" value="false"/> + <param name="matching_window_only" value="false"/> + <param name="irt_mz_extraction_window" value="50.0"/> + <param name="irt_mz_extraction_window_unit" value="ppm"/> + <param name="irt_im_extraction_window" value="-1.0"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="split_file_input" value="false"/> + <param name="use_elution_model_score" value="false"/> + <param name="readOptions" value="workingInMemory"/> + <param name="mz_correction_function" value="none"/> + <param name="extraction_function" value="tophat"/> + <param name="batchSize" value="1000"/> + <param name="ms1_isotopes" value="3"/> + <param name="force" value="false"/> + <param name="test" value="false"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> + <param name="tr" value="OpenSwathWorkflow_17_input.pqp.tmp"/> + <param name="tr_type" value="pqp"/> + <output name="out_features" file="OpenSwathWorkflow_17_b_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_chrom" file="OpenSwathWorkflow_17_b_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="sonar" value="false"/> + <param name="rt_extraction_window" value="600.0"/> + <param name="ion_mobility_window" value="0.05"/> + <param name="mz_extraction_window" value="50.0"/> + <param name="mz_extraction_window_ms1" value="50.0"/> + <param name="im_extraction_window_ms1" value="-1.0"/> + <section name="Debugging"/> + <section name="Calibration"> + <param name="ms1_im_calibration" value="false"/> + <param name="im_correction_function" value="linear"/> + <param name="debug_im_file" value=""/> + <param name="debug_mz_file" value=""/> + </section> + <section name="Library"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <section name="RTNormalization"> + <param name="alignmentMethod" value="linear"/> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + <param name="estimateBestPeptides" value="false"/> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + <section name="lowess"> + <param name="span" value="0.05"/> + </section> + <section name="b_spline"> + <param name="num_nodes" value="5"/> + </section> + </section> + <section name="Scoring"> + <param name="stop_report_after_feature" value="5"/> + <param name="rt_normalization_factor" value="100.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="true"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="0.75"/> + <param name="minimal_quality" value="-1.5"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="11"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="30.0"/> + <param name="use_gauss" value="false"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="0.1"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="max_iteration" value="10"/> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="true"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> + <param name="sort_swath_maps" value="false"/> + <param name="enable_ms1" value="true"/> + <param name="enable_ipf" value="true"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="extra_rt_extraction_window" value="0.0"/> + <param name="mz_extraction_window_unit" value="Th"/> + <param name="mz_extraction_window_ms1_unit" value="ppm"/> + <param name="use_ms1_ion_mobility" value="true"/> + <param name="matching_window_only" value="false"/> + <param name="irt_mz_extraction_window" value="50.0"/> + <param name="irt_mz_extraction_window_unit" value="ppm"/> + <param name="irt_im_extraction_window" value="-1.0"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="split_file_input" value="false"/> + <param name="use_elution_model_score" value="false"/> + <param name="readOptions" value="normal"/> + <param name="mz_correction_function" value="none"/> + <param name="extraction_function" value="tophat"/> + <param name="batchSize" value="1000"/> + <param name="ms1_isotopes" value="0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> + <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> + <param name="tr_type" value=""/> + <output name="out_features" file="OpenSwathWorkflow_18_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="sonar" value="false"/> + <param name="rt_extraction_window" value="600.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_extraction_window" value="0.05"/> + <param name="mz_extraction_window_ms1" value="50.0"/> + <param name="im_extraction_window_ms1" value="-1.0"/> + <section name="Debugging"/> + <section name="Calibration"> + <param name="ms1_im_calibration" value="false"/> + <param name="im_correction_function" value="linear"/> + <param name="debug_im_file" value=""/> + <param name="debug_mz_file" value=""/> + </section> + <section name="Library"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <section name="RTNormalization"> + <param name="alignmentMethod" value="linear"/> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + <param name="estimateBestPeptides" value="false"/> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + <section name="lowess"> + <param name="span" value="0.05"/> + </section> + <section name="b_spline"> + <param name="num_nodes" value="5"/> + </section> + </section> + <section name="Scoring"> + <param name="stop_report_after_feature" value="5"/> + <param name="rt_normalization_factor" value="100.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="true"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="0.75"/> + <param name="minimal_quality" value="-1.5"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="true"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="11"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="30.0"/> + <param name="use_gauss" value="false"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="0.1"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="max_iteration" value="10"/> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="false"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="true"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> + <param name="sort_swath_maps" value="false"/> + <param name="enable_ms1" value="true"/> + <param name="enable_ipf" value="true"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="extra_rt_extraction_window" value="0.0"/> + <param name="mz_extraction_window_unit" value="Th"/> + <param name="mz_extraction_window_ms1_unit" value="ppm"/> + <param name="use_ms1_ion_mobility" value="true"/> + <param name="matching_window_only" value="false"/> + <param name="irt_mz_extraction_window" value="50.0"/> + <param name="irt_mz_extraction_window_unit" value="ppm"/> + <param name="irt_im_extraction_window" value="-1.0"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="split_file_input" value="false"/> + <param name="use_elution_model_score" value="false"/> + <param name="readOptions" value="normal"/> + <param name="mz_correction_function" value="none"/> + <param name="extraction_function" value="tophat"/> + <param name="batchSize" value="1000"/> + <param name="ms1_isotopes" value="0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> + <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> + <param name="tr_type" value=""/> + <output name="out_features" file="OpenSwathWorkflow_19_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="sonar" value="false"/> + <param name="rt_extraction_window" value="600.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_extraction_window" value="0.05"/> + <param name="mz_extraction_window_ms1" value="50.0"/> + <param name="im_extraction_window_ms1" value="-1.0"/> + <section name="Debugging"/> + <section name="Calibration"> + <param name="ms1_im_calibration" value="false"/> + <param name="im_correction_function" value="linear"/> + <param name="debug_im_file" value=""/> + <param name="debug_mz_file" value=""/> + </section> + <section name="Library"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <section name="RTNormalization"> + <param name="alignmentMethod" value="linear"/> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + <param name="estimateBestPeptides" value="false"/> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + <section name="lowess"> + <param name="span" value="0.05"/> + </section> + <section name="b_spline"> + <param name="num_nodes" value="5"/> + </section> + </section> + <section name="Scoring"> + <param name="stop_report_after_feature" value="5"/> + <param name="rt_normalization_factor" value="100.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="true"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="0.75"/> + <param name="minimal_quality" value="-1.5"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="true"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="11"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="30.0"/> + <param name="use_gauss" value="false"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="0.1"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="max_iteration" value="10"/> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="false"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> + <param name="sort_swath_maps" value="false"/> + <param name="enable_ms1" value="true"/> + <param name="enable_ipf" value="true"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="extra_rt_extraction_window" value="0.0"/> + <param name="mz_extraction_window_unit" value="Th"/> + <param name="mz_extraction_window_ms1_unit" value="ppm"/> + <param name="use_ms1_ion_mobility" value="true"/> + <param name="matching_window_only" value="false"/> + <param name="irt_mz_extraction_window" value="50.0"/> + <param name="irt_mz_extraction_window_unit" value="ppm"/> + <param name="irt_im_extraction_window" value="-1.0"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="split_file_input" value="false"/> + <param name="use_elution_model_score" value="false"/> + <param name="readOptions" value="normal"/> + <param name="mz_correction_function" value="none"/> + <param name="extraction_function" value="tophat"/> + <param name="batchSize" value="1000"/> + <param name="ms1_isotopes" value="0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> + <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> + <param name="tr_type" value=""/> + <output name="out_features" file="OpenSwathWorkflow_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="sonar" value="false"/> + <param name="rt_extraction_window" value="600.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_extraction_window" value="0.05"/> + <param name="mz_extraction_window_ms1" value="50.0"/> + <param name="im_extraction_window_ms1" value="-1.0"/> + <section name="Debugging"/> + <section name="Calibration"> + <param name="ms1_im_calibration" value="false"/> + <param name="im_correction_function" value="linear"/> + <param name="debug_im_file" value=""/> + <param name="debug_mz_file" value=""/> + </section> + <section name="Library"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <section name="RTNormalization"> + <param name="alignmentMethod" value="linear"/> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + <param name="estimateBestPeptides" value="false"/> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + <section name="lowess"> + <param name="span" value="0.05"/> + </section> + <section name="b_spline"> + <param name="num_nodes" value="5"/> + </section> + </section> + <section name="Scoring"> + <param name="stop_report_after_feature" value="5"/> + <param name="rt_normalization_factor" value="100.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="true"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="0.75"/> + <param name="minimal_quality" value="-1.5"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="true"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="11"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="30.0"/> + <param name="use_gauss" value="false"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="0.1"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="max_iteration" value="10"/> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="true"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="false"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="4"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="sort_swath_maps" value="false"/> + <param name="enable_ms1" value="true"/> + <param name="enable_ipf" value="true"/> + <param name="out_chrom_type" value="mzML"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="extra_rt_extraction_window" value="0.0"/> + <param name="mz_extraction_window_unit" value="Th"/> + <param name="mz_extraction_window_ms1_unit" value="ppm"/> + <param name="use_ms1_ion_mobility" value="true"/> + <param name="matching_window_only" value="false"/> + <param name="irt_mz_extraction_window" value="50.0"/> + <param name="irt_mz_extraction_window_unit" value="ppm"/> + <param name="irt_im_extraction_window" value="-1.0"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="split_file_input" value="false"/> + <param name="use_elution_model_score" value="false"/> + <param name="readOptions" value="normal"/> + <param name="mz_correction_function" value="none"/> + <param name="extraction_function" value="tophat"/> + <param name="batchSize" value="1000"/> + <param name="ms1_isotopes" value="0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_21_input.mzML"/> + <param name="tr" value="OpenSwathWorkflow_21_input.tsv" ftype="tabular"/> + <param name="tr_type" value=""/> + <param name="tr_irt" value="OpenSwathWorkflow_21_input.irt.TraML"/> + <output name="out_features" file="OpenSwathWorkflow_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_chrom" file="OpenSwathWorkflow_21_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="sonar" value="false"/> + <param name="rt_extraction_window" value="600.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_extraction_window" value="0.05"/> + <param name="mz_extraction_window_ms1" value="50.0"/> + <param name="im_extraction_window_ms1" value="-1.0"/> + <section name="Debugging"/> + <output name="Debugging_irt_trafo" file="OpenSwathWorkflow_21_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> + <section name="Calibration"> + <param name="ms1_im_calibration" value="false"/> + <param name="im_correction_function" value="linear"/> + <param name="debug_im_file" value=""/> + <param name="debug_mz_file" value=""/> + </section> + <section name="Library"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <section name="RTNormalization"> + <param name="alignmentMethod" value="linear"/> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + <param name="estimateBestPeptides" value="false"/> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + <section name="lowess"> + <param name="span" value="0.6666666666666666"/> + </section> + <section name="b_spline"> + <param name="num_nodes" value="5"/> + </section> + </section> + <section name="Scoring"> + <param name="stop_report_after_feature" value="5"/> + <param name="rt_normalization_factor" value="100.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="true"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="0.75"/> + <param name="minimal_quality" value="-1.5"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="true"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="11"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="30.0"/> + <param name="use_gauss" value="false"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="0.1"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="max_iteration" value="10"/> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="true"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="false"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,irt_trafo_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="sort_swath_maps" value="false"/> + <param name="enable_ms1" value="true"/> + <param name="enable_ipf" value="true"/> + <param name="out_chrom_type" value="mzML"/> + <param name="min_upper_edge_dist" value="0.0"/> + <param name="extra_rt_extraction_window" value="0.0"/> + <param name="mz_extraction_window_unit" value="ppm"/> + <param name="mz_extraction_window_ms1_unit" value="ppm"/> + <param name="use_ms1_ion_mobility" value="true"/> + <param name="matching_window_only" value="true"/> + <param name="irt_mz_extraction_window" value="50.0"/> + <param name="irt_mz_extraction_window_unit" value="ppm"/> + <param name="irt_im_extraction_window" value="-1.0"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="split_file_input" value="false"/> + <param name="use_elution_model_score" value="false"/> + <param name="readOptions" value="workingInMemory"/> + <param name="mz_correction_function" value="none"/> + <param name="extraction_function" value="tophat"/> + <param name="batchSize" value="1000"/> + <param name="ms1_isotopes" value="3"/> + <param name="force" value="false"/> + <param name="test" value="false"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_22_input.mzML"/> + <param name="tr" value="OpenSwathWorkflow_22_input.tsv" ftype="tabular"/> + <param name="tr_type" value=""/> + <output name="out_features" file="OpenSwathWorkflow_22_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <output name="out_chrom" file="OpenSwathWorkflow_22_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="sonar" value="false"/> + <param name="rt_extraction_window" value="600.0"/> + <param name="ion_mobility_window" value="-1.0"/> + <param name="mz_extraction_window" value="50.0"/> + <param name="mz_extraction_window_ms1" value="50.0"/> + <param name="im_extraction_window_ms1" value="-1.0"/> + <section name="Debugging"/> + <section name="Calibration"> + <param name="ms1_im_calibration" value="false"/> + <param name="im_correction_function" value="linear"/> + <param name="debug_im_file" value=""/> + <param name="debug_mz_file" value=""/> + </section> + <section name="Library"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <section name="RTNormalization"> + <param name="alignmentMethod" value="linear"/> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + <param name="estimateBestPeptides" value="false"/> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + <section name="lowess"> + <param name="span" value="0.05"/> + </section> + <section name="b_spline"> + <param name="num_nodes" value="5"/> + </section> + </section> + <section name="Scoring"> + <param name="stop_report_after_feature" value="5"/> + <param name="rt_normalization_factor" value="100.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="min_peak_width" value="-1.0"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="true"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="0.75"/> + <param name="minimal_quality" value="-1.5"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="11"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="30.0"/> + <param name="use_gauss" value="false"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="0.1"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="true"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="max_iteration" value="10"/> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="true"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="true"/> + <param name="use_uis_scores" value="false"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_PeakPickerHiRes"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="processOption" value="inmemory"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeakPickerHiRes_input.mzML"/> + <output name="out" file="PeakPickerHiRes_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="signal_to_noise" value="1.0"/> + <param name="spacing_difference_gap" value="4.0"/> + <param name="spacing_difference" value="1.5"/> + <param name="missing" value="1"/> + <param name="ms_levels" value="1"/> + <param name="report_FWHM" value="true"/> + <param name="report_FWHM_unit" value="relative"/> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="processOption" value="inmemory"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeakPickerHiRes_2_input.mzML"/> + <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="signal_to_noise" value="1.0"/> + <param name="spacing_difference_gap" value="4.0"/> + <param name="spacing_difference" value="1.5"/> + <param name="missing" value="1"/> + <param name="ms_levels" value="1"/> + <param name="report_FWHM" value="true"/> + <param name="report_FWHM_unit" value="relative"/> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="processOption" value="lowmemory"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeakPickerHiRes_input.mzML"/> + <output name="out" file="PeakPickerHiRes_output_lowMem.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="signal_to_noise" value="1.0"/> + <param name="spacing_difference_gap" value="4.0"/> + <param name="spacing_difference" value="1.5"/> + <param name="missing" value="1"/> + <param name="ms_levels" value="1"/> + <param name="report_FWHM" value="true"/> + <param name="report_FWHM_unit" value="relative"/> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="processOption" value="lowmemory"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeakPickerHiRes_2_input.mzML"/> + <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="signal_to_noise" value="1.0"/> + <param name="spacing_difference_gap" value="4.0"/> + <param name="spacing_difference" value="1.5"/> + <param name="missing" value="1"/> + <param name="ms_levels" value="1"/> + <param name="report_FWHM" value="true"/> + <param name="report_FWHM_unit" value="relative"/> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="processOption" value="inmemory"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeakPickerHiRes_5_input.mzML"/> + <output name="out" file="PeakPickerHiRes_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="signal_to_noise" value="0.0"/> + <param name="spacing_difference_gap" value="4.0"/> + <param name="spacing_difference" value="1.5"/> + <param name="missing" value="1"/> + <param name="ms_levels" value=""/> + <param name="report_FWHM" value="false"/> + <param name="report_FWHM_unit" value="relative"/> + <section name="SignalToNoise"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + <param name="write_log_messages" value="true"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_PeakPickerIterative"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeakPickerIterative_1_input.mzML"/> + <output name="out" file="PeakPickerIterative_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="signal_to_noise_" value="1.0"/> + <param name="peak_width" value="0.04"/> + <param name="spacing_difference" value="1.5"/> + <param name="sn_bin_count_" value="30"/> + <param name="nr_iterations_" value="5"/> + <param name="sn_win_len_" value="20.0"/> + <param name="check_width_internally" value="false"/> + <param name="ms1_only" value="false"/> + <param name="clear_meta_data" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeakPickerIterative_2_input.mzML"/> + <output name="out" file="PeakPickerIterative_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="signal_to_noise_" value="0.0"/> + <param name="peak_width" value="0.04"/> + <param name="spacing_difference" value="2.5"/> + <param name="sn_bin_count_" value="30"/> + <param name="nr_iterations_" value="5"/> + <param name="sn_win_len_" value="20.0"/> + <param name="check_width_internally" value="true"/> + <param name="ms1_only" value="false"/> + <param name="clear_meta_data" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_PeakPickerWavelet"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="write_peak_meta_data" value="true"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeakPickerWavelet_input.mzML"/> + <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="signal_to_noise" value="3.0"/> + <param name="centroid_percentage" value="0.6"/> + <param name="peak_width" value="0.2"/> + <param name="estimate_peak_width" value="false"/> + <param name="fwhm_lower_bound_factor" value="0.5"/> + <param name="fwhm_upper_bound_factor" value="20.0"/> + <section name="optimization"> + <param name="iterations" value="400"/> + <section name="penalties"> + <param name="position" value="0.0"/> + <param name="left_width" value="1.0"/> + <param name="right_width" value="1.0"/> + <param name="height" value="1.0"/> + </section> + <section name="2d"> + <param name="tolerance_mz" value="2.2"/> + <param name="max_peak_distance" value="1.2"/> + </section> + </section> + <section name="thresholds"> + <param name="peak_bound" value="100.0"/> + <param name="peak_bound_ms2_level" value="10.0"/> + <param name="correlation" value="0.5"/> + <param name="noise_level" value="0.1"/> + <param name="search_radius" value="3"/> + </section> + <section name="wavelet_transform"> + <param name="spacing" value="0.001"/> + </section> + <section name="deconvolution"> + <param name="deconvolution" value="false"/> + <param name="asym_threshold" value="0.3"/> + <param name="left_width" value="2.0"/> + <param name="right_width" value="2.0"/> + <param name="scaling" value="0.12"/> + <section name="fitting"> + <param name="fwhm_threshold" value="0.7"/> + <param name="eps_abs" value="9.999999747378752e-06"/> + <param name="eps_rel" value="9.999999747378752e-06"/> + <param name="max_iteration" value="10"/> + <section name="penalties"> + <param name="position" value="0.0"/> + <param name="height" value="1.0"/> + <param name="left_width" value="0.0"/> + <param name="right_width" value="0.0"/> + </section> + </section> + </section> + <section name="SignalToNoiseEstimationParameter"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="stdev_mp" value="3.0"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="write_peak_meta_data" value="true"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeakPickerWavelet_deconv_input.mzML"/> + <output name="out" file="PeakPickerWavelet_deconv_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="signal_to_noise" value="2.0"/> + <param name="centroid_percentage" value="0.8"/> + <param name="peak_width" value="0.15"/> + <param name="estimate_peak_width" value="false"/> + <param name="fwhm_lower_bound_factor" value="1.0"/> + <param name="fwhm_upper_bound_factor" value="20.0"/> + <section name="optimization"> + <param name="iterations" value="400"/> + <section name="penalties"> + <param name="position" value="0.0"/> + <param name="left_width" value="1.0"/> + <param name="right_width" value="1.0"/> + <param name="height" value="1.0"/> + </section> + <section name="2d"> + <param name="tolerance_mz" value="2.2"/> + <param name="max_peak_distance" value="1.2"/> + </section> + </section> + <section name="thresholds"> + <param name="peak_bound" value="200.0"/> + <param name="peak_bound_ms2_level" value="50.0"/> + <param name="correlation" value="0.5"/> + <param name="noise_level" value="0.1"/> + <param name="search_radius" value="3"/> + </section> + <section name="wavelet_transform"> + <param name="spacing" value="0.001"/> + </section> + <section name="deconvolution"> + <param name="deconvolution" value="true"/> + <param name="asym_threshold" value="0.3"/> + <param name="left_width" value="2.0"/> + <param name="right_width" value="2.0"/> + <param name="scaling" value="0.1"/> + <section name="fitting"> + <param name="fwhm_threshold" value="0.7"/> + <param name="eps_abs" value="9.999999747378752e-06"/> + <param name="eps_rel" value="9.999999747378752e-06"/> + <param name="max_iteration" value="100"/> + <section name="penalties"> + <param name="position" value="1.0"/> + <param name="height" value="1.0"/> + <param name="left_width" value="0.0"/> + <param name="right_width" value="0.0"/> + </section> + </section> + </section> + <section name="SignalToNoiseEstimationParameter"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="stdev_mp" value="3.0"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="write_peak_meta_data" value="true"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeakPickerWavelet_input.mzML"/> + <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="signal_to_noise" value="3.0"/> + <param name="centroid_percentage" value="0.6"/> + <param name="peak_width" value="0.2"/> + <param name="estimate_peak_width" value="false"/> + <param name="fwhm_lower_bound_factor" value="0.5"/> + <param name="fwhm_upper_bound_factor" value="20.0"/> + <section name="optimization"> + <param name="iterations" value="400"/> + <section name="penalties"> + <param name="position" value="0.0"/> + <param name="left_width" value="1.0"/> + <param name="right_width" value="1.0"/> + <param name="height" value="1.0"/> + </section> + <section name="2d"> + <param name="tolerance_mz" value="2.2"/> + <param name="max_peak_distance" value="1.2"/> + </section> + </section> + <section name="thresholds"> + <param name="peak_bound" value="100.0"/> + <param name="peak_bound_ms2_level" value="10.0"/> + <param name="correlation" value="0.5"/> + <param name="noise_level" value="0.1"/> + <param name="search_radius" value="3"/> + </section> + <section name="wavelet_transform"> + <param name="spacing" value="0.001"/> + </section> + <section name="deconvolution"> + <param name="deconvolution" value="false"/> + <param name="asym_threshold" value="0.3"/> + <param name="left_width" value="2.0"/> + <param name="right_width" value="2.0"/> + <param name="scaling" value="0.12"/> + <section name="fitting"> + <param name="fwhm_threshold" value="0.7"/> + <param name="eps_abs" value="9.999999747378752e-06"/> + <param name="eps_rel" value="9.999999747378752e-06"/> + <param name="max_iteration" value="10"/> + <section name="penalties"> + <param name="position" value="0.0"/> + <param name="height" value="1.0"/> + <param name="left_width" value="0.0"/> + <param name="right_width" value="0.0"/> + </section> + </section> + </section> + <section name="SignalToNoiseEstimationParameter"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="stdev_mp" value="3.0"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="write_peak_meta_data" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeakPickerWavelet_input.mzML"/> + <output name="out" file="PeakPickerWavelet_output_noMetaData.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="signal_to_noise" value="3.0"/> + <param name="centroid_percentage" value="0.6"/> + <param name="peak_width" value="0.2"/> + <param name="estimate_peak_width" value="false"/> + <param name="fwhm_lower_bound_factor" value="0.5"/> + <param name="fwhm_upper_bound_factor" value="20.0"/> + <section name="optimization"> + <param name="iterations" value="400"/> + <section name="penalties"> + <param name="position" value="0.0"/> + <param name="left_width" value="1.0"/> + <param name="right_width" value="1.0"/> + <param name="height" value="1.0"/> + </section> + <section name="2d"> + <param name="tolerance_mz" value="2.2"/> + <param name="max_peak_distance" value="1.2"/> + </section> + </section> + <section name="thresholds"> + <param name="peak_bound" value="100.0"/> + <param name="peak_bound_ms2_level" value="10.0"/> + <param name="correlation" value="0.5"/> + <param name="noise_level" value="0.1"/> + <param name="search_radius" value="3"/> + </section> + <section name="wavelet_transform"> + <param name="spacing" value="0.001"/> + </section> + <section name="deconvolution"> + <param name="deconvolution" value="false"/> + <param name="asym_threshold" value="0.3"/> + <param name="left_width" value="2.0"/> + <param name="right_width" value="2.0"/> + <param name="scaling" value="0.12"/> + <section name="fitting"> + <param name="fwhm_threshold" value="0.7"/> + <param name="eps_abs" value="9.999999747378752e-06"/> + <param name="eps_rel" value="9.999999747378752e-06"/> + <param name="max_iteration" value="10"/> + <section name="penalties"> + <param name="position" value="0.0"/> + <param name="height" value="1.0"/> + <param name="left_width" value="0.0"/> + <param name="right_width" value="0.0"/> + </section> + </section> + </section> + <section name="SignalToNoiseEstimationParameter"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="stdev_mp" value="3.0"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_PepNovoAdapter"> +</xml> + <xml name="autotest_PeptideIndexer"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeptideIndexer_1.idXML"/> + <param name="fasta" value="PeptideIndexer_1.fasta"/> + <output name="out" file="PeptideIndexer_1_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="decoy_string" value=""/> + <param name="decoy_string_position" value="prefix"/> + <param name="missing_decoy_action" value="error"/> + <param name="write_protein_sequence" value="false"/> + <param name="write_protein_description" value="false"/> + <param name="keep_unreferenced_proteins" value="false"/> + <param name="unmatched_action" value="warn"/> + <param name="aaa_max" value="4"/> + <param name="mismatches_max" value="0"/> + <param name="IL_equivalent" value="false"/> + <section name="enzyme"> + <param name="name" value="auto"/> + <param name="specificity" value="none"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeptideIndexer_1.idXML"/> + <param name="fasta" value="PeptideIndexer_1.fasta"/> + <output name="out" file="PeptideIndexer_2_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="decoy_string" value=""/> + <param name="decoy_string_position" value="prefix"/> + <param name="missing_decoy_action" value="error"/> + <param name="write_protein_sequence" value="true"/> + <param name="write_protein_description" value="false"/> + <param name="keep_unreferenced_proteins" value="false"/> + <param name="unmatched_action" value="warn"/> + <param name="aaa_max" value="4"/> + <param name="mismatches_max" value="0"/> + <param name="IL_equivalent" value="false"/> + <section name="enzyme"> + <param name="name" value="auto"/> + <param name="specificity" value="none"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeptideIndexer_1.idXML"/> + <param name="fasta" value="PeptideIndexer_1.fasta"/> + <output name="out" file="PeptideIndexer_3_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="decoy_string" value=""/> + <param name="decoy_string_position" value="prefix"/> + <param name="missing_decoy_action" value="error"/> + <param name="write_protein_sequence" value="false"/> + <param name="write_protein_description" value="false"/> + <param name="keep_unreferenced_proteins" value="true"/> + <param name="unmatched_action" value="warn"/> + <param name="aaa_max" value="4"/> + <param name="mismatches_max" value="0"/> + <param name="IL_equivalent" value="false"/> + <section name="enzyme"> + <param name="name" value="auto"/> + <param name="specificity" value="none"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeptideIndexer_1.idXML"/> + <param name="fasta" value="PeptideIndexer_1.fasta"/> + <output name="out" file="PeptideIndexer_4_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="decoy_string" value=""/> + <param name="decoy_string_position" value="prefix"/> + <param name="missing_decoy_action" value="error"/> + <param name="write_protein_sequence" value="true"/> + <param name="write_protein_description" value="false"/> + <param name="keep_unreferenced_proteins" value="false"/> + <param name="unmatched_action" value="warn"/> + <param name="aaa_max" value="0"/> + <param name="mismatches_max" value="0"/> + <param name="IL_equivalent" value="false"/> + <section name="enzyme"> + <param name="name" value="auto"/> + <param name="specificity" value="none"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeptideIndexer_1.idXML"/> + <param name="fasta" value="PeptideIndexer_1.fasta"/> + <output name="out" file="PeptideIndexer_5_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="decoy_string" value=""/> + <param name="decoy_string_position" value="prefix"/> + <param name="missing_decoy_action" value="error"/> + <param name="write_protein_sequence" value="false"/> + <param name="write_protein_description" value="false"/> + <param name="keep_unreferenced_proteins" value="false"/> + <param name="unmatched_action" value="warn"/> + <param name="aaa_max" value="4"/> + <param name="mismatches_max" value="0"/> + <param name="IL_equivalent" value="false"/> + <section name="enzyme"> + <param name="name" value="auto"/> + <param name="specificity" value="none"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeptideIndexer_2.idXML"/> + <param name="fasta" value="PeptideIndexer_1.fasta"/> + <output name="out" file="PeptideIndexer_6_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="decoy_string" value=""/> + <param name="decoy_string_position" value="prefix"/> + <param name="missing_decoy_action" value="error"/> + <param name="write_protein_sequence" value="false"/> + <param name="write_protein_description" value="false"/> + <param name="keep_unreferenced_proteins" value="false"/> + <param name="unmatched_action" value="warn"/> + <param name="aaa_max" value="3"/> + <param name="mismatches_max" value="0"/> + <param name="IL_equivalent" value="false"/> + <section name="enzyme"> + <param name="name" value="auto"/> + <param name="specificity" value="none"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeptideIndexer_3.idXML"/> + <param name="fasta" value="PeptideIndexer_1.fasta"/> + <output name="out" file="PeptideIndexer_7_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="decoy_string" value="DECOY_"/> + <param name="decoy_string_position" value="prefix"/> + <param name="missing_decoy_action" value="error"/> + <param name="write_protein_sequence" value="false"/> + <param name="write_protein_description" value="false"/> + <param name="keep_unreferenced_proteins" value="false"/> + <param name="unmatched_action" value="warn"/> + <param name="aaa_max" value="4"/> + <param name="mismatches_max" value="0"/> + <param name="IL_equivalent" value="false"/> + <section name="enzyme"> + <param name="name" value="auto"/> + <param name="specificity" value="full"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeptideIndexer_3.idXML"/> + <param name="fasta" value="PeptideIndexer_1.fasta"/> + <output name="out" file="PeptideIndexer_8_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="decoy_string" value=""/> + <param name="decoy_string_position" value="prefix"/> + <param name="missing_decoy_action" value="error"/> + <param name="write_protein_sequence" value="false"/> + <param name="write_protein_description" value="false"/> + <param name="keep_unreferenced_proteins" value="false"/> + <param name="unmatched_action" value="warn"/> + <param name="aaa_max" value="4"/> + <param name="mismatches_max" value="0"/> + <param name="IL_equivalent" value="false"/> + <section name="enzyme"> + <param name="name" value="auto"/> + <param name="specificity" value="semi"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeptideIndexer_3.idXML"/> + <param name="fasta" value="PeptideIndexer_1.fasta"/> + <output name="out" file="PeptideIndexer_9_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="decoy_string" value=""/> + <param name="decoy_string_position" value="prefix"/> + <param name="missing_decoy_action" value="error"/> + <param name="write_protein_sequence" value="false"/> + <param name="write_protein_description" value="false"/> + <param name="keep_unreferenced_proteins" value="false"/> + <param name="unmatched_action" value="remove"/> + <param name="aaa_max" value="4"/> + <param name="mismatches_max" value="0"/> + <param name="IL_equivalent" value="false"/> + <section name="enzyme"> + <param name="name" value="auto"/> + <param name="specificity" value="none"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeptideIndexer_10_input.idXML"/> + <param name="fasta" value="PeptideIndexer_10_input.fasta"/> + <output name="out" file="PeptideIndexer_10_output.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="decoy_string" value=""/> + <param name="decoy_string_position" value="prefix"/> + <param name="missing_decoy_action" value="error"/> + <param name="write_protein_sequence" value="true"/> + <param name="write_protein_description" value="false"/> + <param name="keep_unreferenced_proteins" value="false"/> + <param name="unmatched_action" value="error"/> + <param name="aaa_max" value="3"/> + <param name="mismatches_max" value="0"/> + <param name="IL_equivalent" value="true"/> + <section name="enzyme"> + <param name="name" value="auto"/> + <param name="specificity" value="auto"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeptideIndexer_1.idXML"/> + <param name="fasta" value="PeptideIndexer_1.fasta"/> + <output name="out" file="PeptideIndexer_12_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="decoy_string" value=""/> + <param name="decoy_string_position" value="prefix"/> + <param name="missing_decoy_action" value="error"/> + <param name="write_protein_sequence" value="false"/> + <param name="write_protein_description" value="false"/> + <param name="keep_unreferenced_proteins" value="false"/> + <param name="unmatched_action" value="warn"/> + <param name="aaa_max" value="4"/> + <param name="mismatches_max" value="0"/> + <param name="IL_equivalent" value="false"/> + <section name="enzyme"> + <param name="name" value="auto"/> + <param name="specificity" value="none"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="empty.idXML"/> + <param name="fasta" value="PeptideIndexer_1.fasta"/> + <output name="out" file="PeptideIndexer_13_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="decoy_string" value=""/> + <param name="decoy_string_position" value="prefix"/> + <param name="missing_decoy_action" value="error"/> + <param name="write_protein_sequence" value="false"/> + <param name="write_protein_description" value="false"/> + <param name="keep_unreferenced_proteins" value="false"/> + <param name="unmatched_action" value="error"/> + <param name="aaa_max" value="4"/> + <param name="mismatches_max" value="0"/> + <param name="IL_equivalent" value="false"/> + <section name="enzyme"> + <param name="name" value="auto"/> + <param name="specificity" value="auto"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PeptideIndexer_14.idXML"/> + <param name="fasta" value="PeptideIndexer_2.fasta"/> + <output name="out" file="PeptideIndexer_14_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="decoy_string" value=""/> + <param name="decoy_string_position" value="prefix"/> + <param name="missing_decoy_action" value="error"/> + <param name="write_protein_sequence" value="true"/> + <param name="write_protein_description" value="false"/> + <param name="keep_unreferenced_proteins" value="false"/> + <param name="unmatched_action" value="error"/> + <param name="aaa_max" value="4"/> + <param name="mismatches_max" value="0"/> + <param name="IL_equivalent" value="false"/> + <section name="enzyme"> + <param name="name" value="auto"/> + <param name="specificity" value="none"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_PercolatorAdapter"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="generic_feature_set" value="false"/> + <param name="subset_max_train" value="0"/> + <param name="cpos" value="0.0"/> + <param name="cneg" value="0.0"/> + <param name="testFDR" value="0.5"/> + <param name="trainFDR" value="0.5"/> + <param name="maxiter" value="10"/> + <param name="nested_xval_bins" value="1"/> + <param name="quick_validation" value="false"/> + <param name="static" value="false"/> + <param name="default_direction" value=""/> + <param name="verbose" value="2"/> + <param name="unitnorm" value="false"/> + <param name="test_each_iteration" value="false"/> + <param name="override" value="false"/> + <param name="seed" value="1"/> + <param name="doc" value="0"/> + <param name="klammer" value="false"/> + <param name="decoy_pattern" value="random"/> + <param name="post_processing_tdc" value="false"/> + <param name="train_best_positive" value="false"/> + <param name="ipf_max_peakgroup_pep" value="0.7"/> + <param name="ipf_max_transition_isotope_overlap" value="0.5"/> + <param name="ipf_min_transition_sn" value="0.0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PercolatorAdapter_1.idXML"/> + <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="enzyme" value="trypsin"/> + <param name="peptide_level_fdrs" value="false"/> + <param name="protein_level_fdrs" value="false"/> + <param name="osw_level" value="ms2"/> + <param name="score_type" value="q-value"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="generic_feature_set" value="false"/> + <param name="subset_max_train" value="0"/> + <param name="cpos" value="0.0"/> + <param name="cneg" value="0.0"/> + <param name="testFDR" value="0.01"/> + <param name="trainFDR" value="0.01"/> + <param name="maxiter" value="10"/> + <param name="nested_xval_bins" value="1"/> + <param name="quick_validation" value="false"/> + <param name="static" value="false"/> + <param name="default_direction" value=""/> + <param name="verbose" value="2"/> + <param name="unitnorm" value="false"/> + <param name="test_each_iteration" value="false"/> + <param name="override" value="false"/> + <param name="seed" value="1"/> + <param name="doc" value="0"/> + <param name="klammer" value="false"/> + <param name="decoy_pattern" value="random"/> + <param name="post_processing_tdc" value="false"/> + <param name="train_best_positive" value="false"/> + <param name="ipf_max_peakgroup_pep" value="0.7"/> + <param name="ipf_max_transition_isotope_overlap" value="0.5"/> + <param name="ipf_min_transition_sn" value="0.0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in_osw" value="PercolatorAdapter_2.osw"/> + <output name="out" file="PercolatorAdapter_2_out1.osw" compare="sim_size" delta="5700" ftype="osw"/> + <param name="out_type" value="osw"/> + <param name="enzyme" value="trypsin"/> + <param name="peptide_level_fdrs" value="false"/> + <param name="protein_level_fdrs" value="false"/> + <param name="osw_level" value="ms1"/> + <param name="score_type" value="q-value"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="generic_feature_set" value="false"/> + <param name="subset_max_train" value="0"/> + <param name="cpos" value="0.0"/> + <param name="cneg" value="0.0"/> + <param name="testFDR" value="0.01"/> + <param name="trainFDR" value="0.01"/> + <param name="maxiter" value="10"/> + <param name="nested_xval_bins" value="1"/> + <param name="quick_validation" value="false"/> + <param name="static" value="false"/> + <param name="default_direction" value=""/> + <param name="verbose" value="2"/> + <param name="unitnorm" value="false"/> + <param name="test_each_iteration" value="false"/> + <param name="override" value="false"/> + <param name="seed" value="1"/> + <param name="doc" value="0"/> + <param name="klammer" value="false"/> + <param name="decoy_pattern" value="random"/> + <param name="post_processing_tdc" value="false"/> + <param name="train_best_positive" value="false"/> + <param name="ipf_max_peakgroup_pep" value="0.7"/> + <param name="ipf_max_transition_isotope_overlap" value="0.5"/> + <param name="ipf_min_transition_sn" value="0.0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in_osw" value="PercolatorAdapter_2_out1.osw"/> + <output name="out" file="PercolatorAdapter_3_out1.osw" compare="sim_size" delta="5700" ftype="osw"/> + <param name="out_type" value="osw"/> + <param name="enzyme" value="trypsin"/> + <param name="peptide_level_fdrs" value="false"/> + <param name="protein_level_fdrs" value="false"/> + <param name="osw_level" value="ms2"/> + <param name="score_type" value="q-value"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="generic_feature_set" value="false"/> + <param name="subset_max_train" value="0"/> + <param name="cpos" value="0.0"/> + <param name="cneg" value="0.0"/> + <param name="testFDR" value="0.01"/> + <param name="trainFDR" value="0.01"/> + <param name="maxiter" value="10"/> + <param name="nested_xval_bins" value="1"/> + <param name="quick_validation" value="false"/> + <param name="static" value="false"/> + <param name="default_direction" value=""/> + <param name="verbose" value="2"/> + <param name="unitnorm" value="false"/> + <param name="test_each_iteration" value="false"/> + <param name="override" value="false"/> + <param name="seed" value="1"/> + <param name="doc" value="0"/> + <param name="klammer" value="false"/> + <param name="decoy_pattern" value="random"/> + <param name="post_processing_tdc" value="false"/> + <param name="train_best_positive" value="false"/> + <param name="ipf_max_peakgroup_pep" value="0.7"/> + <param name="ipf_max_transition_isotope_overlap" value="0.5"/> + <param name="ipf_min_transition_sn" value="0.0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in_osw" value="PercolatorAdapter_3_out1.osw"/> + <output name="out" file="PercolatorAdapter_4_out1.osw" compare="sim_size" delta="5700" ftype="osw"/> + <param name="out_type" value="osw"/> + <param name="enzyme" value="trypsin"/> + <param name="peptide_level_fdrs" value="false"/> + <param name="protein_level_fdrs" value="false"/> + <param name="osw_level" value="transition"/> + <param name="score_type" value="q-value"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="generic_feature_set" value="false"/> + <param name="subset_max_train" value="0"/> + <param name="cpos" value="0.0"/> + <param name="cneg" value="0.0"/> + <param name="testFDR" value="0.5"/> + <param name="trainFDR" value="0.5"/> + <param name="maxiter" value="10"/> + <param name="nested_xval_bins" value="1"/> + <param name="quick_validation" value="false"/> + <param name="static" value="false"/> + <param name="default_direction" value=""/> + <param name="verbose" value="2"/> + <param name="unitnorm" value="false"/> + <param name="test_each_iteration" value="false"/> + <param name="override" value="false"/> + <param name="seed" value="1"/> + <param name="doc" value="0"/> + <param name="klammer" value="false"/> + <param name="decoy_pattern" value="random"/> + <param name="post_processing_tdc" value="false"/> + <param name="train_best_positive" value="false"/> + <param name="ipf_max_peakgroup_pep" value="0.7"/> + <param name="ipf_max_transition_isotope_overlap" value="0.5"/> + <param name="ipf_min_transition_sn" value="0.0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PercolatorAdapter_1.idXML"/> + <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <output name="out_pin" file="PercolatorAdapter_1_out1.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="out_type" value="idXML"/> + <param name="enzyme" value="trypsin"/> + <param name="peptide_level_fdrs" value="false"/> + <param name="protein_level_fdrs" value="false"/> + <param name="osw_level" value="ms2"/> + <param name="score_type" value="q-value"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_pin_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_PhosphoScoring"> +</xml> + <xml name="autotest_PrecursorIonSelector"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="solver" value="GLPK"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PrecursorIonSelector_features.featureXML"/> + <param name="ids" value="PrecursorIonSelector_ids.idXML"/> + <param name="num_precursors" value="1"/> + <param name="load_preprocessing" value="false"/> + <param name="store_preprocessing" value="false"/> + <param name="simulation" value="true"/> + <output name="sim_results" file="PrecursorIonSelector_1_output.txt" compare="sim_size" delta="5700" ftype="txt"/> + <param name="db_path" value="PrecursorIonSelector_db.fasta"/> + <param name="fixed_modifications" value=""/> + <section name="algorithm"> + <param name="type" value="IPS"/> + <param name="max_iteration" value="10"/> + <param name="rt_bin_capacity" value="10"/> + <param name="step_size" value="1"/> + <param name="peptide_min_prob" value="0.2"/> + <param name="sequential_spectrum_order" value="false"/> + <section name="MIPFormulation"> + <section name="thresholds"> + <param name="min_protein_probability" value="0.2"/> + <param name="min_protein_id_probability" value="0.95"/> + <param name="min_pt_weight" value="0.5"/> + <param name="min_mz" value="500.0"/> + <param name="max_mz" value="5000.0"/> + <param name="min_pred_pep_prob" value="0.5"/> + <param name="min_rt_weight" value="0.5"/> + <param name="use_peptide_rule" value="true"/> + <param name="min_peptide_ids" value="2"/> + <param name="min_peptide_probability" value="0.95"/> + </section> + <section name="combined_ilp"> + <param name="k1" value="0.2"/> + <param name="k2" value="0.2"/> + <param name="k3" value="0.4"/> + <param name="scale_matching_probs" value="true"/> + </section> + <section name="feature_based"> + <param name="no_intensity_normalization" value="false"/> + <param name="max_number_precursors_per_feature" value="1"/> + </section> + </section> + <section name="Preprocessing"> + <param name="precursor_mass_tolerance" value="0.9"/> + <param name="precursor_mass_tolerance_unit" value="Da"/> + <param name="preprocessed_db_path" value=""/> + <param name="preprocessed_db_pred_rt_path" value=""/> + <param name="preprocessed_db_pred_dt_path" value=""/> + <param name="max_peptides_per_run" value="100000"/> + <param name="missed_cleavages" value="1"/> + <param name="taxonomy" value=""/> + <param name="store_peptide_sequences" value="false"/> + <section name="rt_settings"> + <param name="min_rt" value="960.0"/> + <param name="max_rt" value="3840.0"/> + <param name="rt_step_size" value="30.0"/> + <param name="gauss_mean" value="-1.0"/> + <param name="gauss_sigma" value="3.0"/> + </section> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,sim_results_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="solver" value="GLPK"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PrecursorIonSelector_features.featureXML"/> + <output name="out" file="PrecursorIonSelector_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="ids" value="PrecursorIonSelector_ids.idXML"/> + <param name="num_precursors" value="1"/> + <param name="load_preprocessing" value="false"/> + <param name="store_preprocessing" value="false"/> + <param name="simulation" value="false"/> + <param name="db_path" value="PrecursorIonSelector_db.fasta"/> + <param name="fixed_modifications" value=""/> + <section name="algorithm"> + <param name="type" value="IPS"/> + <param name="max_iteration" value="10"/> + <param name="rt_bin_capacity" value="10"/> + <param name="step_size" value="1"/> + <param name="peptide_min_prob" value="0.2"/> + <param name="sequential_spectrum_order" value="false"/> + <section name="MIPFormulation"> + <section name="thresholds"> + <param name="min_protein_probability" value="0.2"/> + <param name="min_protein_id_probability" value="0.95"/> + <param name="min_pt_weight" value="0.5"/> + <param name="min_mz" value="500.0"/> + <param name="max_mz" value="5000.0"/> + <param name="min_pred_pep_prob" value="0.5"/> + <param name="min_rt_weight" value="0.5"/> + <param name="use_peptide_rule" value="true"/> + <param name="min_peptide_ids" value="2"/> + <param name="min_peptide_probability" value="0.95"/> + </section> + <section name="combined_ilp"> + <param name="k1" value="0.2"/> + <param name="k2" value="0.2"/> + <param name="k3" value="0.4"/> + <param name="scale_matching_probs" value="true"/> + </section> + <section name="feature_based"> + <param name="no_intensity_normalization" value="false"/> + <param name="max_number_precursors_per_feature" value="1"/> + </section> + </section> + <section name="Preprocessing"> + <param name="precursor_mass_tolerance" value="0.9"/> + <param name="precursor_mass_tolerance_unit" value="Da"/> + <param name="preprocessed_db_path" value=""/> + <param name="preprocessed_db_pred_rt_path" value=""/> + <param name="preprocessed_db_pred_dt_path" value=""/> + <param name="max_peptides_per_run" value="100000"/> + <param name="missed_cleavages" value="1"/> + <param name="taxonomy" value=""/> + <param name="store_peptide_sequences" value="false"/> + <section name="rt_settings"> + <param name="min_rt" value="960.0"/> + <param name="max_rt" value="3840.0"/> + <param name="rt_step_size" value="30.0"/> + <param name="gauss_mean" value="-1.0"/> + <param name="gauss_sigma" value="3.0"/> + </section> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_PrecursorMassCorrector"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="max_charge" value="3"/> + <param name="intensity_threshold" value="-1.0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PrecursorMassCorrector_1_input.mzML"/> + <output name="out" file="PrecursorMassCorrector_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="precursor_mass_tolerance" value="1.5"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_ProteinInference"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ProteinInference_1_input.idXML"/> + <output name="out" file="ProteinInference_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="merge_runs" value="all"/> + <param name="annotate_indist_groups" value="true"/> + <section name="Merging"> + <param name="annotate_origin" value="false"/> + <param name="allow_disagreeing_settings" value="false"/> + </section> + <section name="Algorithm"> + <param name="min_peptides_per_protein" value="1"/> + <param name="score_aggregation_method" value="maximum"/> + <param name="treat_charge_variants_separately" value="true"/> + <param name="treat_modification_variants_separately" value="true"/> + <param name="use_shared_peptides" value="false"/> + <param name="skip_count_annotation" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_ProteinQuantifier"> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ProteinQuantifier_input.featureXML"/> + <output name="out" file="ProteinQuantifier_1_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> + <output name="peptide_out" file="ProteinQuantifier_1_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> + <param name="top" value="3"/> + <param name="average" value="median"/> + <param name="include_all" value="false"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="false"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ProteinQuantifier_input.featureXML"/> + <output name="out" file="ProteinQuantifier_2_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> + <output name="peptide_out" file="ProteinQuantifier_2_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> + <param name="top" value="2"/> + <param name="average" value="sum"/> + <param name="include_all" value="true"/> + <param name="best_charge_and_fraction" value="true"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="false"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ProteinQuantifier_3_input.featureXML"/> + <output name="out" file="ProteinQuantifier_3_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> + <output name="peptide_out" file="ProteinQuantifier_3_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> + <param name="top" value="2"/> + <param name="average" value="mean"/> + <param name="include_all" value="true"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="false"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ProteinQuantifier_input.consensusXML"/> + <output name="out" file="ProteinQuantifier_4_output.txt" compare="sim_size" delta="5700" ftype="csv"/> + <param name="top" value="0"/> + <param name="average" value="sum"/> + <param name="include_all" value="false"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="false"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ProteinQuantifier_input.consensusXML"/> + <output name="out" file="ProteinQuantifier_5_output.txt" compare="sim_size" delta="5700" ftype="csv"/> + <param name="top" value="3"/> + <param name="average" value="sum"/> + <param name="include_all" value="false"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="false"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ProteinQuantifier_input.consensusXML"/> + <output name="out" file="ProteinQuantifier_6_output.txt" compare="sim_size" delta="5700" ftype="csv"/> + <param name="top" value="3"/> + <param name="average" value="sum"/> + <param name="include_all" value="true"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="false"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ProteinQuantifier_input.consensusXML"/> + <output name="out" file="ProteinQuantifier_7_output.txt" compare="sim_size" delta="5700" ftype="csv"/> + <param name="top" value="0"/> + <param name="average" value="sum"/> + <param name="include_all" value="false"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="true"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ProteinQuantifier_input.consensusXML"/> + <output name="out" file="ProteinQuantifier_8_output.txt" compare="sim_size" delta="5700" ftype="csv"/> + <param name="top" value="3"/> + <param name="average" value="sum"/> + <param name="include_all" value="false"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="true"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ProteinQuantifier_input.consensusXML"/> + <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/> + <output name="mztab" file="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> + <param name="top" value="3"/> + <param name="average" value="sum"/> + <param name="include_all" value="true"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="true"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mztab_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ProteinQuantifier_input.consensusXML"/> + <output name="out" file="ProteinQuantifier_12_output.txt" compare="sim_size" delta="5700" ftype="csv"/> + <param name="top" value="3"/> + <param name="average" value="sum"/> + <param name="include_all" value="true"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="true"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="true"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ProteinQuantifier_input.consensusXML"/> + <output name="out" file="ProteinQuantifier_13_output.txt" compare="sim_size" delta="5700" ftype="csv"/> + <param name="top" value="3"/> + <param name="average" value="sum"/> + <param name="include_all" value="true"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="true"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="true"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ProteinQuantifier_input.idXML"/> + <output name="out" file="ProteinQuantifier_14_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> + <output name="peptide_out" file="ProteinQuantifier_14_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> + <param name="top" value="0"/> + <param name="average" value="sum"/> + <param name="include_all" value="false"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="false"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_ProteinResolver"> + <test expect_num_outputs="4"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="fasta" value="ProteinResolver_1_input.fasta"/> + <param name="in" value="ProteinResolver_1_input.consensusXML"/> + <param name="in_path" value=""/> + <output name="protein_groups" file="ProteinResolver_1_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> + <output name="peptide_table" file="ProteinResolver_1_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> + <output name="protein_table" file="ProteinResolver_1_output3.txt" compare="sim_size" delta="5700" ftype="csv"/> + <section name="resolver"> + <param name="missed_cleavages" value="2"/> + <param name="min_length" value="6"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="designer"> + <param name="experiment" value="ExperimentalSetting"/> + <param name="file" value="File"/> + <param name="separator" value="tab"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,protein_groups_FLAG,peptide_table_FLAG,protein_table_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_PSMFeatureExtractor"> +</xml> + <xml name="autotest_PTModel"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in_positive" value="PTModel_1_input_positive.idXML"/> + <param name="in_negative" value="PTModel_1_input_negative.idXML"/> + <output name="out" file="PTModel_1_output.tmp" compare="sim_size" delta="5700" ftype="txt"/> + <param name="c" value="0.5"/> + <param name="svm_type" value="C_SVC"/> + <param name="nu" value="0.5"/> + <param name="kernel_type" value="OLIGO"/> + <param name="degree" value="1"/> + <param name="border_length" value="22"/> + <param name="k_mer_length" value="1"/> + <param name="sigma" value="5.0"/> + <param name="max_positive_count" value="1000"/> + <param name="max_negative_count" value="1000"/> + <param name="redundant" value="false"/> + <param name="additive_cv" value="false"/> + <section name="cv"> + <param name="skip_cv" value="true"/> + <param name="number_of_runs" value="10"/> + <param name="number_of_partitions" value="10"/> + <param name="degree_start" value="1"/> + <param name="degree_step_size" value="2"/> + <param name="degree_stop" value="4"/> + <param name="c_start" value="1.0"/> + <param name="c_step_size" value="100.0"/> + <param name="c_stop" value="1000.0"/> + <param name="nu_start" value="0.1"/> + <param name="nu_step_size" value="1.3"/> + <param name="nu_stop" value="0.9"/> + <param name="sigma_start" value="1.0"/> + <param name="sigma_step_size" value="1.3"/> + <param name="sigma_stop" value="15.0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_QCCalculator"> +</xml> + <xml name="autotest_QCEmbedder"> +</xml> + <xml name="autotest_QCExporter"> +</xml> + <xml name="autotest_QCExtractor"> +</xml> + <xml name="autotest_QCImporter"> +</xml> + <xml name="autotest_QCMerger"> +</xml> + <xml name="autotest_QCShrinker"> +</xml> + <xml name="autotest_QualityControl"> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in_cm" value="QualityControl_1_in.consensusXML"/> + <param name="in_raw" value="QualityControl_1_in1.mzML.gz,QualityControl_1_in2.mzML.gz,QualityControl_1_in3.mzML.gz"/> + <param name="in_postFDR" value="QualityControl_1_in1.featureXML,QualityControl_1_in2.featureXML,QualityControl_1_in3.featureXML"/> + <output name="out" file="QualityControl_1_out.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> + <output name="out_cm" file="QualityControl_1_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> + <param name="in_contaminants" value="QualityControl_1.fasta"/> + <param name="in_trafo" value="QualityControl_1_in1.trafoXML,QualityControl_1_in2.trafoXML,QualityControl_1_in3.trafoXML"/> + <section name="FragmentMassError"> + <param name="unit" value="auto"/> + <param name="tolerance" value="20.0"/> + </section> + <section name="MS2_id_rate"> + <param name="assume_all_target" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_cm_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_RNADigestor"> +</xml> + <xml name="autotest_RNAMassCalculator"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in_seq" value=""AUCGGC""/> + <output name="out" file="RNAMassCalculator_1.txt" compare="sim_size" delta="5700" ftype="txt"/> + <param name="charge" value="-1 -2"/> + <param name="format" value="list"/> + <param name="average_mass" value="false"/> + <param name="fragment_type" value="full"/> + <param name="separator" value=""/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_RNPxlSearch"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="RNPxlSearch_1_input.mzML"/> + <param name="database" value="RNPxlSearch_1_input.fasta"/> + <output name="out" file="RNPxlSearch_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <section name="precursor"> + <param name="mass_tolerance" value="20.0"/> + <param name="mass_tolerance_unit" value="ppm"/> + <param name="min_charge" value="2"/> + <param name="max_charge" value="5"/> + <param name="isotopes" value="0 1"/> + </section> + <section name="fragment"> + <param name="mass_tolerance" value="20.0"/> + <param name="mass_tolerance_unit" value="ppm"/> + </section> + <section name="modifications"> + <param name="fixed" value=""/> + <param name="variable" value="Oxidation (M)"/> + <param name="variable_max_per_peptide" value="2"/> + </section> + <section name="peptide"> + <param name="min_size" value="6"/> + <param name="max_size" value="1000000"/> + <param name="missed_cleavages" value="1"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="report"> + <param name="top_hits" value="1"/> + </section> + <section name="RNPxl"> + <param name="length" value="2"/> + <param name="sequence" value="GUA"/> + <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> + <param name="nt_groups" value=""/> + <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> + <param name="can_cross_link" value="U"/> + <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> + <param name="modifications" value=""U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3""/> + <param name="scoring" value="fast"/> + <param name="decoys" value="false"/> + <param name="CysteineAdduct" value="false"/> + <param name="filter_fractional_mass" value="false"/> + <param name="carbon_labeled_fragments" value="false"/> + <param name="only_xl" value="false"/> + <param name="filter_small_peptide_mass" value="600.0"/> + <param name="marker_ions_tolerance" value="0.05"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="RNPxlSearch_1_input.mzML"/> + <param name="database" value="RNPxlSearch_1_input.fasta"/> + <output name="out" file="RNPxlSearch_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <section name="precursor"> + <param name="mass_tolerance" value="20.0"/> + <param name="mass_tolerance_unit" value="ppm"/> + <param name="min_charge" value="2"/> + <param name="max_charge" value="5"/> + <param name="isotopes" value="0 1"/> + </section> + <section name="fragment"> + <param name="mass_tolerance" value="20.0"/> + <param name="mass_tolerance_unit" value="ppm"/> + </section> + <section name="modifications"> + <param name="fixed" value=""/> + <param name="variable" value="Oxidation (M)"/> + <param name="variable_max_per_peptide" value="2"/> + </section> + <section name="peptide"> + <param name="min_size" value="6"/> + <param name="max_size" value="1000000"/> + <param name="missed_cleavages" value="1"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="report"> + <param name="top_hits" value="1"/> + </section> + <section name="RNPxl"> + <param name="length" value="2"/> + <param name="sequence" value="GUA"/> + <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> + <param name="nt_groups" value=""/> + <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> + <param name="can_cross_link" value="U"/> + <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> + <param name="modifications" value=""U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3""/> + <param name="scoring" value="fast"/> + <param name="decoys" value="true"/> + <param name="CysteineAdduct" value="false"/> + <param name="filter_fractional_mass" value="false"/> + <param name="carbon_labeled_fragments" value="false"/> + <param name="only_xl" value="false"/> + <param name="filter_small_peptide_mass" value="600.0"/> + <param name="marker_ions_tolerance" value="0.05"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="RNPxlSearch_1_input.mzML"/> + <param name="database" value="RNPxlSearch_1_input.fasta"/> + <output name="out" file="RNPxlSearch_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <output name="out_tsv" file="RNPxlSearch_3_output2.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <section name="precursor"> + <param name="mass_tolerance" value="10.0"/> + <param name="mass_tolerance_unit" value="ppm"/> + <param name="min_charge" value="2"/> + <param name="max_charge" value="5"/> + <param name="isotopes" value="0 1"/> + </section> + <section name="fragment"> + <param name="mass_tolerance" value="10.0"/> + <param name="mass_tolerance_unit" value="ppm"/> + </section> + <section name="modifications"> + <param name="fixed" value=""/> + <param name="variable" value=""/> + <param name="variable_max_per_peptide" value="2"/> + </section> + <section name="peptide"> + <param name="min_size" value="6"/> + <param name="max_size" value="1000000"/> + <param name="missed_cleavages" value="1"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="report"> + <param name="top_hits" value="3"/> + </section> + <section name="RNPxl"> + <param name="length" value="2"/> + <param name="sequence" value=""/> + <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> + <param name="nt_groups" value=""/> + <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> + <param name="can_cross_link" value="U"/> + <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> + <param name="modifications" value=""U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3""/> + <param name="scoring" value="fast"/> + <param name="decoys" value="false"/> + <param name="CysteineAdduct" value="false"/> + <param name="filter_fractional_mass" value="false"/> + <param name="carbon_labeled_fragments" value="false"/> + <param name="only_xl" value="false"/> + <param name="filter_small_peptide_mass" value="600.0"/> + <param name="marker_ions_tolerance" value="0.05"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="RNPxlSearch_1_input.mzML"/> + <param name="database" value="RNPxlSearch_1_input.fasta"/> + <output name="out" file="RNPxlSearch_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <output name="out_tsv" file="RNPxlSearch_4_output2.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <section name="precursor"> + <param name="mass_tolerance" value="10.0"/> + <param name="mass_tolerance_unit" value="ppm"/> + <param name="min_charge" value="2"/> + <param name="max_charge" value="5"/> + <param name="isotopes" value="0 1"/> + </section> + <section name="fragment"> + <param name="mass_tolerance" value="10.0"/> + <param name="mass_tolerance_unit" value="ppm"/> + </section> + <section name="modifications"> + <param name="fixed" value=""/> + <param name="variable" value=""/> + <param name="variable_max_per_peptide" value="2"/> + </section> + <section name="peptide"> + <param name="min_size" value="6"/> + <param name="max_size" value="1000000"/> + <param name="missed_cleavages" value="1"/> + <param name="enzyme" value="Trypsin"/> + </section> + <section name="report"> + <param name="top_hits" value="2"/> + </section> + <section name="RNPxl"> + <param name="length" value="2"/> + <param name="sequence" value=""/> + <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> + <param name="nt_groups" value=""/> + <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> + <param name="can_cross_link" value="U"/> + <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> + <param name="modifications" value=""U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3""/> + <param name="scoring" value="fast"/> + <param name="decoys" value="true"/> + <param name="CysteineAdduct" value="false"/> + <param name="filter_fractional_mass" value="false"/> + <param name="carbon_labeled_fragments" value="false"/> + <param name="only_xl" value="false"/> + <param name="filter_small_peptide_mass" value="600.0"/> + <param name="marker_ions_tolerance" value="0.05"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_RNPxlXICFilter"> +</xml> + <xml name="autotest_RTEvaluation"> +</xml> + <xml name="autotest_RTModel"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="RTModel_1_input.idXML"/> + <output name="out" file="RTModel_1_output.model" compare="sim_size" delta="5700" ftype="txt"/> + <param name="svm_type" value="NU_SVR"/> + <param name="nu" value="0.5"/> + <param name="p" value="0.1"/> + <param name="c" value="0.1"/> + <param name="kernel_type" value="POLY"/> + <param name="degree" value="1"/> + <param name="border_length" value="22"/> + <param name="max_std" value="10.0"/> + <param name="k_mer_length" value="1"/> + <param name="sigma" value="5.0"/> + <param name="total_gradient_time" value="3000.0"/> + <param name="first_dim_rt" value="false"/> + <param name="additive_cv" value="false"/> + <section name="cv"> + <param name="skip_cv" value="true"/> + <param name="number_of_runs" value="10"/> + <param name="number_of_partitions" value="10"/> + <param name="degree_start" value="1"/> + <param name="degree_step_size" value="2"/> + <param name="degree_stop" value="4"/> + <param name="p_start" value="1.0"/> + <param name="p_step_size" value="10.0"/> + <param name="p_stop" value="1000.0"/> + <param name="c_start" value="1.0"/> + <param name="c_step_size" value="10.0"/> + <param name="c_stop" value="1000.0"/> + <param name="nu_start" value="0.3"/> + <param name="nu_step_size" value="1.2"/> + <param name="nu_stop" value="0.7"/> + <param name="sigma_start" value="1.0"/> + <param name="sigma_step_size" value="1.3"/> + <param name="sigma_stop" value="15.0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in_positive" value="RTModel_2_input_positive.idXML"/> + <param name="in_negative" value="RTModel_2_input_negative.idXML"/> + <output name="out" file="RTModel_2_output.tmp" compare="sim_size" delta="5700" ftype="txt"/> + <param name="svm_type" value="NU_SVR"/> + <param name="nu" value="0.5"/> + <param name="p" value="0.1"/> + <param name="c" value="0.5"/> + <param name="kernel_type" value="OLIGO"/> + <param name="degree" value="1"/> + <param name="border_length" value="22"/> + <param name="max_std" value="10.0"/> + <param name="k_mer_length" value="1"/> + <param name="sigma" value="5.0"/> + <param name="total_gradient_time" value="1.0"/> + <param name="first_dim_rt" value="false"/> + <param name="additive_cv" value="false"/> + <section name="cv"> + <param name="skip_cv" value="true"/> + <param name="number_of_runs" value="10"/> + <param name="number_of_partitions" value="10"/> + <param name="degree_start" value="1"/> + <param name="degree_step_size" value="2"/> + <param name="degree_stop" value="4"/> + <param name="p_start" value="1.0"/> + <param name="p_step_size" value="10.0"/> + <param name="p_stop" value="1000.0"/> + <param name="c_start" value="1.0"/> + <param name="c_step_size" value="10.0"/> + <param name="c_stop" value="1000.0"/> + <param name="nu_start" value="0.3"/> + <param name="nu_step_size" value="1.2"/> + <param name="nu_stop" value="0.7"/> + <param name="sigma_start" value="1.0"/> + <param name="sigma_step_size" value="1.3"/> + <param name="sigma_stop" value="15.0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="RTModel_3_input.idXML"/> + <output name="out" file="RTModel_3_output.tmp" compare="sim_size" delta="5700" ftype="txt"/> + <param name="svm_type" value="NU_SVR"/> + <param name="nu" value="0.5"/> + <param name="p" value="0.1"/> + <param name="c" value="0.001953125"/> + <param name="kernel_type" value="OLIGO"/> + <param name="degree" value="1"/> + <param name="border_length" value="22"/> + <param name="max_std" value="10.0"/> + <param name="k_mer_length" value="1"/> + <param name="sigma" value="1.0"/> + <param name="total_gradient_time" value="1.0"/> + <param name="first_dim_rt" value="false"/> + <param name="additive_cv" value="false"/> + <section name="cv"> + <param name="skip_cv" value="false"/> + <param name="number_of_runs" value="1"/> + <param name="number_of_partitions" value="5"/> + <param name="degree_start" value="1"/> + <param name="degree_step_size" value="2"/> + <param name="degree_stop" value="4"/> + <param name="p_start" value="1.0"/> + <param name="p_step_size" value="10.0"/> + <param name="p_stop" value="1000.0"/> + <param name="c_start" value="0.001953125"/> + <param name="c_step_size" value="2.0"/> + <param name="c_stop" value="0.001953125"/> + <param name="nu_start" value="0.4"/> + <param name="nu_step_size" value="1.2"/> + <param name="nu_stop" value="0.4"/> + <param name="sigma_start" value="5.0"/> + <param name="sigma_step_size" value="1.221055"/> + <param name="sigma_stop" value="5.0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="RTModel_4_input.txt" ftype="txt"/> + <output name="out" file="RTModel_4_output.tmp" compare="sim_size" delta="5700" ftype="txt"/> + <param name="svm_type" value="NU_SVR"/> + <param name="nu" value="0.5"/> + <param name="p" value="0.1"/> + <param name="c" value="0.001953125"/> + <param name="kernel_type" value="OLIGO"/> + <param name="degree" value="1"/> + <param name="border_length" value="22"/> + <param name="max_std" value="10.0"/> + <param name="k_mer_length" value="1"/> + <param name="sigma" value="1.0"/> + <param name="total_gradient_time" value="1.0"/> + <param name="first_dim_rt" value="false"/> + <param name="additive_cv" value="false"/> + <section name="cv"> + <param name="skip_cv" value="false"/> + <param name="number_of_runs" value="1"/> + <param name="number_of_partitions" value="5"/> + <param name="degree_start" value="1"/> + <param name="degree_step_size" value="2"/> + <param name="degree_stop" value="4"/> + <param name="p_start" value="1.0"/> + <param name="p_step_size" value="10.0"/> + <param name="p_stop" value="1000.0"/> + <param name="c_start" value="0.001953125"/> + <param name="c_step_size" value="2.0"/> + <param name="c_stop" value="0.001953125"/> + <param name="nu_start" value="0.4"/> + <param name="nu_step_size" value="1.2"/> + <param name="nu_stop" value="0.4"/> + <param name="sigma_start" value="5.0"/> + <param name="sigma_step_size" value="1.221055"/> + <param name="sigma_stop" value="5.0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_SeedListGenerator"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="PepXMLFile_test.mzML"/> + <output name="out" file="SeedListGenerator_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="use_peptide_mass" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDMapper_1_output.featureXML"/> + <output name="out" file="SeedListGenerator_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> + <param name="use_peptide_mass" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_SemanticValidator"> +</xml> + <xml name="autotest_SequenceCoverageCalculator"> +</xml> + <xml name="autotest_SimpleSearchEngine"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="SimpleSearchEngine_1.mzML"/> + <param name="database" value="SimpleSearchEngine_1.fasta"/> + <output name="out" file="SimpleSearchEngine_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <section name="Search"> + <param name="enzyme" value="Trypsin"/> + <param name="decoys" value="false"/> + <section name="precursor"> + <param name="mass_tolerance" value="5.0"/> + <param name="mass_tolerance_unit" value="ppm"/> + <param name="min_charge" value="2"/> + <param name="max_charge" value="5"/> + <param name="isotopes" value="0 1"/> + </section> + <section name="fragment"> + <param name="mass_tolerance" value="0.3"/> + <param name="mass_tolerance_unit" value="Da"/> + </section> + <section name="modifications"> + <param name="fixed" value=""/> + <param name="variable" value="Oxidation (M)"/> + <param name="variable_max_per_peptide" value="2"/> + </section> + <section name="annotate"> + <param name="PSM" value=""/> + </section> + <section name="peptide"> + <param name="min_size" value="7"/> + <param name="max_size" value="40"/> + <param name="missed_cleavages" value="1"/> + <param name="motif" value=""/> + </section> + <section name="report"> + <param name="top_hits" value="1"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_SiriusAdapter"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="converter_mode" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="SiriusAdapter_1_input.mzML"/> + <output name="out_sirius" file="SiriusAdapter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> + <param name="out_workspace_directory" value=""/> + <section name="preprocessing"> + <param name="filter_by_num_masstraces" value="1"/> + <param name="precursor_mz_tolerance" value="0.005"/> + <param name="precursor_mz_tolerance_unit" value="Da"/> + <param name="precursor_rt_tolerance" value="5"/> + <param name="isotope_pattern_iterations" value="3"/> + <param name="feature_only" value="false"/> + <param name="no_masstrace_info_isotope_pattern" value="false"/> + </section> + <section name="sirius"> + <param name="profile" value="qtof"/> + <param name="candidates" value="5"/> + <param name="database" value="all"/> + <param name="noise" value="0"/> + <param name="ppm_max" value="10"/> + <param name="isotope" value="both"/> + <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> + <param name="compound_timeout" value="10"/> + <param name="tree_timeout" value="0"/> + <param name="top_n_hits" value="10"/> + <param name="auto_charge" value="true"/> + <param name="ion_tree" value="false"/> + <param name="no_recalibration" value="false"/> + <param name="most_intense_ms2" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="converter_mode" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="SiriusAdapter_2_input.mzML"/> + <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/> + <output name="out_sirius" file="SiriusAdapter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> + <param name="out_workspace_directory" value=""/> + <section name="preprocessing"> + <param name="filter_by_num_masstraces" value="3"/> + <param name="precursor_mz_tolerance" value="0.005"/> + <param name="precursor_mz_tolerance_unit" value="Da"/> + <param name="precursor_rt_tolerance" value="5"/> + <param name="isotope_pattern_iterations" value="3"/> + <param name="feature_only" value="true"/> + <param name="no_masstrace_info_isotope_pattern" value="false"/> + </section> + <section name="sirius"> + <param name="profile" value="qtof"/> + <param name="candidates" value="5"/> + <param name="database" value="all"/> + <param name="noise" value="0"/> + <param name="ppm_max" value="10"/> + <param name="isotope" value="both"/> + <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> + <param name="compound_timeout" value="10"/> + <param name="tree_timeout" value="0"/> + <param name="top_n_hits" value="10"/> + <param name="auto_charge" value="true"/> + <param name="ion_tree" value="false"/> + <param name="no_recalibration" value="false"/> + <param name="most_intense_ms2" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="converter_mode" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="SiriusAdapter_3_input.mzML"/> + <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/> + <output name="out_sirius" file="SiriusAdapter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> + <param name="out_workspace_directory" value=""/> + <section name="preprocessing"> + <param name="filter_by_num_masstraces" value="3"/> + <param name="precursor_mz_tolerance" value="0.005"/> + <param name="precursor_mz_tolerance_unit" value="Da"/> + <param name="precursor_rt_tolerance" value="5"/> + <param name="isotope_pattern_iterations" value="3"/> + <param name="feature_only" value="false"/> + <param name="no_masstrace_info_isotope_pattern" value="false"/> + </section> + <section name="sirius"> + <param name="profile" value="qtof"/> + <param name="candidates" value="5"/> + <param name="database" value="all"/> + <param name="noise" value="0"/> + <param name="ppm_max" value="10"/> + <param name="isotope" value="both"/> + <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> + <param name="compound_timeout" value="10"/> + <param name="tree_timeout" value="0"/> + <param name="top_n_hits" value="10"/> + <param name="auto_charge" value="true"/> + <param name="ion_tree" value="false"/> + <param name="no_recalibration" value="false"/> + <param name="most_intense_ms2" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="converter_mode" value="true"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="SiriusAdapter_3_input.mzML"/> + <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/> + <output name="out_ms" file="SiriusAdapter_5_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/> + <param name="out_workspace_directory" value=""/> + <section name="preprocessing"> + <param name="filter_by_num_masstraces" value="1"/> + <param name="precursor_mz_tolerance" value="0.005"/> + <param name="precursor_mz_tolerance_unit" value="Da"/> + <param name="precursor_rt_tolerance" value="5"/> + <param name="isotope_pattern_iterations" value="3"/> + <param name="feature_only" value="false"/> + <param name="no_masstrace_info_isotope_pattern" value="false"/> + </section> + <section name="sirius"> + <param name="profile" value="qtof"/> + <param name="candidates" value="5"/> + <param name="database" value="all"/> + <param name="noise" value="0"/> + <param name="ppm_max" value="10"/> + <param name="isotope" value="both"/> + <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> + <param name="compound_timeout" value="10"/> + <param name="tree_timeout" value="0"/> + <param name="top_n_hits" value="10"/> + <param name="auto_charge" value="false"/> + <param name="ion_tree" value="false"/> + <param name="no_recalibration" value="false"/> + <param name="most_intense_ms2" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="converter_mode" value="true"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="SiriusAdapter_4_input.mzML"/> + <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/> + <output name="out_ms" file="SiriusAdapter_6_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/> + <param name="out_workspace_directory" value=""/> + <section name="preprocessing"> + <param name="filter_by_num_masstraces" value="1"/> + <param name="precursor_mz_tolerance" value="0.005"/> + <param name="precursor_mz_tolerance_unit" value="Da"/> + <param name="precursor_rt_tolerance" value="5"/> + <param name="isotope_pattern_iterations" value="3"/> + <param name="feature_only" value="false"/> + <param name="no_masstrace_info_isotope_pattern" value="false"/> + </section> + <section name="sirius"> + <param name="profile" value="qtof"/> + <param name="candidates" value="5"/> + <param name="database" value="all"/> + <param name="noise" value="0"/> + <param name="ppm_max" value="10"/> + <param name="isotope" value="both"/> + <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> + <param name="compound_timeout" value="10"/> + <param name="tree_timeout" value="0"/> + <param name="top_n_hits" value="10"/> + <param name="auto_charge" value="false"/> + <param name="ion_tree" value="false"/> + <param name="no_recalibration" value="false"/> + <param name="most_intense_ms2" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="converter_mode" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="SiriusAdapter_4_input.mzML"/> + <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/> + <output name="out_sirius" file="SiriusAdapter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> + <param name="out_workspace_directory" value=""/> + <section name="preprocessing"> + <param name="filter_by_num_masstraces" value="1"/> + <param name="precursor_mz_tolerance" value="0.005"/> + <param name="precursor_mz_tolerance_unit" value="Da"/> + <param name="precursor_rt_tolerance" value="5"/> + <param name="isotope_pattern_iterations" value="3"/> + <param name="feature_only" value="true"/> + <param name="no_masstrace_info_isotope_pattern" value="false"/> + </section> + <section name="sirius"> + <param name="profile" value="qtof"/> + <param name="candidates" value="5"/> + <param name="database" value="all"/> + <param name="noise" value="0"/> + <param name="ppm_max" value="10"/> + <param name="isotope" value="both"/> + <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> + <param name="compound_timeout" value="10"/> + <param name="tree_timeout" value="0"/> + <param name="top_n_hits" value="10"/> + <param name="auto_charge" value="false"/> + <param name="ion_tree" value="false"/> + <param name="no_recalibration" value="false"/> + <param name="most_intense_ms2" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="converter_mode" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="SiriusAdapter_2_input.mzML"/> + <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/> + <output name="out_sirius" file="SiriusAdapter_4_output.tmp" compare="sim_size" delta="5700" ftype="mztab"/> + <output name="out_fingerid" file="SiriusAdapter_4_foutput.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> + <param name="out_workspace_directory" value=""/> + <section name="preprocessing"> + <param name="filter_by_num_masstraces" value="1"/> + <param name="precursor_mz_tolerance" value="0.005"/> + <param name="precursor_mz_tolerance_unit" value="Da"/> + <param name="precursor_rt_tolerance" value="5"/> + <param name="isotope_pattern_iterations" value="3"/> + <param name="feature_only" value="false"/> + <param name="no_masstrace_info_isotope_pattern" value="false"/> + </section> + <section name="sirius"> + <param name="profile" value="qtof"/> + <param name="candidates" value="5"/> + <param name="database" value="pubchem"/> + <param name="noise" value="0"/> + <param name="ppm_max" value="10"/> + <param name="isotope" value="both"/> + <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> + <param name="compound_timeout" value="10"/> + <param name="tree_timeout" value="0"/> + <param name="top_n_hits" value="10"/> + <param name="auto_charge" value="true"/> + <param name="ion_tree" value="false"/> + <param name="no_recalibration" value="false"/> + <param name="most_intense_ms2" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG,out_fingerid_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_SpecLibCreator"> +</xml> + <xml name="autotest_SpecLibSearcher"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="SpecLibSearcher_1.mzML"/> + <param name="lib" value="SpecLibSearcher_1.MSP"/> + <output_collection name="out" count="1"/> + <param name="compare_function" value="ZhangSimilarityScore"/> + <section name="precursor"> + <param name="mass_tolerance" value="3.0"/> + <param name="mass_tolerance_unit" value="Da"/> + <param name="min_charge" value="1"/> + <param name="max_charge" value="5"/> + <param name="isotopes" value="0 1"/> + </section> + <section name="fragment"> + <param name="mass_tolerance" value="10.0"/> + </section> + <section name="report"> + <param name="top_hits" value="10"/> + </section> + <section name="filter"> + <param name="remove_peaks_below_threshold" value="2.01"/> + <param name="min_peaks" value="5"/> + <param name="max_peaks" value="150"/> + <param name="cut_peaks_below" value="1000"/> + </section> + <section name="modifications"> + <param name="fixed" value=""/> + <param name="variable" value=""/> + <param name="variable_max_per_peptide" value="2"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_SpectraFilterBernNorm"> +</xml> + <xml name="autotest_SpectraFilterMarkerMower"> +</xml> + <xml name="autotest_SpectraFilterNLargest"> +</xml> + <xml name="autotest_SpectraFilterNormalizer"> +</xml> + <xml name="autotest_SpectraFilterParentPeakMower"> +</xml> + <xml name="autotest_SpectraFilterScaler"> +</xml> + <xml name="autotest_SpectraFilterSqrtMower"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> + <output name="out" file="SpectraFilterSqrtMower_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_SpectraFilterThresholdMower"> +</xml> + <xml name="autotest_SpectraFilterWindowMower"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="SpectraFilterWindowMower_1_input.mzML"/> + <output name="out" file="SpectraFilterWindowMower_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="windowsize" value="50.0"/> + <param name="peakcount" value="2"/> + <param name="movetype" value="slide"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="SpectraFilterWindowMower_2_input.mzML"/> + <output name="out" file="SpectraFilterWindowMower_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <section name="algorithm"> + <param name="windowsize" value="20.0"/> + <param name="peakcount" value="4"/> + <param name="movetype" value="slide"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_SpectraMerger"> +</xml> + <xml name="autotest_SpectraSTSearchAdapter"/> + <xml name="autotest_StaticModification"> +</xml> + <xml name="autotest_SvmTheoreticalSpectrumGeneratorTrainer"> +</xml> + <xml name="autotest_TargetedFileConverter"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ConvertTSVToTraML_1_input.tsv" ftype="tabular"/> + <output name="out" file="ConvertTSVToTraML_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/> + <output name="out" file="ConvertTSVToTraML_2_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="minutes"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/> + <output name="out" file="ConvertTSVToTraML_3_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="seconds"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ConvertTSVToTraML_4_input.mrm" ftype="mrm"/> + <output name="out" file="ConvertTSVToTraML_4_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ConvertTSVToTraML_5_input.tsv" ftype="tabular"/> + <output name="out" file="ConvertTSVToTraML_5_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ConvertTSVToTraML_6_input.tsv" ftype="tabular"/> + <output name="out" file="ConvertTSVToTraML_6_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ConvertTSVToTraML_7_input_Skyline.tsv" ftype="tabular"/> + <output name="out" file="ConvertTSVToTraML_7_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/> + <output name="out" file="TargetedFileConverter_1_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="legacy_traml_id" value="true"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/> + <output name="out" file="TargetedFileConverter_2_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/> + <output name="out" file="TargetedFileConverter_3_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="legacy_traml_id" value="true"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/> + <output name="out" file="TargetedFileConverter_4_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="TargetedFileConverter_10_output.TraML.tmp"/> + <output name="out" file="TargetedFileConverter_10_output.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="out_type" value="tsv"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="TargetedFileConverter_11_output.pqp.tmp"/> + <output name="out" file="TargetedFileConverter_11_input.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="TargetedFileConverter_8_output.TraML.tmp"/> + <output name="out" file="TargetedFileConverter_8_input.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="out_type" value="tsv"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="true"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="TargetedFileConverter_9_output.pqp.tmp"/> + <output name="out" file="TargetedFileConverter_9_input.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="true"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ConvertTSVToTraML_output.TraML"/> + <output name="out" file="ConvertTraMLToTSV_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="out_type" value="tsv"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="TargetedFileConverter_12_output.pqp.tmp"/> + <output name="out" file="TargetedFileConverter_12_input.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="true"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="TargetedFileConverter_12_input.tsv" ftype="tabular"/> + <output name="out" file="TargetedFileConverter_13_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="ConvertTSVToTraML_5_output.TraML"/> + <output name="out" file="ConvertTraMLToTSV_output_2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="out_type" value="tsv"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="AssayGeneratorMetabo_ams_uku_output_consensus.tsv" ftype="tabular"/> + <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus_traml.tmp.TraML" compare="sim_size" delta="5700" ftype="traml"/> + <param name="out_type" value="traml"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_TextExporter"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="TextExporter_1_input.featureXML"/> + <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="separator" value=""/> + <param name="replacement" value="_"/> + <param name="quoting" value="none"/> + <param name="no_ids" value="false"/> + <section name="feature"> + <param name="minimal" value="false"/> + <param name="add_metavalues" value="-1"/> + </section> + <section name="id"> + <param name="proteins_only" value="false"/> + <param name="peptides_only" value="false"/> + <param name="protein_groups" value="false"/> + <param name="first_dim_rt" value="false"/> + <param name="add_metavalues" value="-1"/> + <param name="add_hit_metavalues" value="-1"/> + <param name="add_protein_hit_metavalues" value="-1"/> + </section> + <section name="consensus"> + <param name="sorting_method" value="none"/> + <param name="sort_by_maps" value="false"/> + <param name="sort_by_size" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="5"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="TextExporter_2_input.consensusXML"/> + <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="separator" value=""/> + <param name="replacement" value="_"/> + <param name="quoting" value="none"/> + <param name="no_ids" value="true"/> + <section name="feature"> + <param name="minimal" value="false"/> + <param name="add_metavalues" value="-1"/> + </section> + <section name="id"> + <param name="proteins_only" value="false"/> + <param name="peptides_only" value="false"/> + <param name="protein_groups" value="false"/> + <param name="first_dim_rt" value="false"/> + <param name="add_metavalues" value="-1"/> + <param name="add_hit_metavalues" value="-1"/> + <param name="add_protein_hit_metavalues" value="-1"/> + </section> + <section name="consensus"> + <param name="sorting_method" value="RT_then_MZ"/> + <param name="sort_by_maps" value="true"/> + <param name="sort_by_size" value="true"/> + </section> + <output name="consensus_centroids" file="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta="5700" ftype="csv"/> + <output name="consensus_elements" file="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta="5700" ftype="csv"/> + <output name="consensus_features" file="TextExporter_2_consensus_features.tmp" compare="sim_size" delta="5700" ftype="csv"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="TextExporter_3_input.idXML"/> + <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="separator" value=""/> + <param name="replacement" value="_"/> + <param name="quoting" value="none"/> + <param name="no_ids" value="false"/> + <section name="feature"> + <param name="minimal" value="false"/> + <param name="add_metavalues" value="-1"/> + </section> + <section name="id"> + <param name="proteins_only" value="false"/> + <param name="peptides_only" value="false"/> + <param name="protein_groups" value="false"/> + <param name="first_dim_rt" value="false"/> + <param name="add_metavalues" value="-1"/> + <param name="add_hit_metavalues" value="-1"/> + <param name="add_protein_hit_metavalues" value="-1"/> + </section> + <section name="consensus"> + <param name="sorting_method" value="none"/> + <param name="sort_by_maps" value="false"/> + <param name="sort_by_size" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="TextExporter_3_input.idXML"/> + <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="separator" value=""/> + <param name="replacement" value="_"/> + <param name="quoting" value="none"/> + <param name="no_ids" value="false"/> + <section name="feature"> + <param name="minimal" value="false"/> + <param name="add_metavalues" value="-1"/> + </section> + <section name="id"> + <param name="proteins_only" value="true"/> + <param name="peptides_only" value="false"/> + <param name="protein_groups" value="false"/> + <param name="first_dim_rt" value="false"/> + <param name="add_metavalues" value="-1"/> + <param name="add_hit_metavalues" value="-1"/> + <param name="add_protein_hit_metavalues" value="-1"/> + </section> + <section name="consensus"> + <param name="sorting_method" value="none"/> + <param name="sort_by_maps" value="false"/> + <param name="sort_by_size" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="TextExporter_5_input.idXML"/> + <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="separator" value=""/> + <param name="replacement" value="_"/> + <param name="quoting" value="none"/> + <param name="no_ids" value="false"/> + <section name="feature"> + <param name="minimal" value="false"/> + <param name="add_metavalues" value="-1"/> + </section> + <section name="id"> + <param name="proteins_only" value="false"/> + <param name="peptides_only" value="true"/> + <param name="protein_groups" value="false"/> + <param name="first_dim_rt" value="true"/> + <param name="add_metavalues" value="-1"/> + <param name="add_hit_metavalues" value="-1"/> + <param name="add_protein_hit_metavalues" value="-1"/> + </section> + <section name="consensus"> + <param name="sorting_method" value="none"/> + <param name="sort_by_maps" value="false"/> + <param name="sort_by_size" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="TextExporter_6_input.featureXML"/> + <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="separator" value=""/> + <param name="replacement" value="_"/> + <param name="quoting" value="none"/> + <param name="no_ids" value="true"/> + <section name="feature"> + <param name="minimal" value="false"/> + <param name="add_metavalues" value="-1"/> + </section> + <section name="id"> + <param name="proteins_only" value="false"/> + <param name="peptides_only" value="false"/> + <param name="protein_groups" value="false"/> + <param name="first_dim_rt" value="false"/> + <param name="add_metavalues" value="-1"/> + <param name="add_hit_metavalues" value="-1"/> + <param name="add_protein_hit_metavalues" value="-1"/> + </section> + <section name="consensus"> + <param name="sorting_method" value="none"/> + <param name="sort_by_maps" value="false"/> + <param name="sort_by_size" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="TextExporter_7_input.consensusXML"/> + <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="separator" value=""/> + <param name="replacement" value="_"/> + <param name="quoting" value="none"/> + <param name="no_ids" value="false"/> + <section name="feature"> + <param name="minimal" value="false"/> + <param name="add_metavalues" value="-1"/> + </section> + <section name="id"> + <param name="proteins_only" value="false"/> + <param name="peptides_only" value="false"/> + <param name="protein_groups" value="false"/> + <param name="first_dim_rt" value="false"/> + <param name="add_metavalues" value="-1"/> + <param name="add_hit_metavalues" value="-1"/> + <param name="add_protein_hit_metavalues" value="-1"/> + </section> + <section name="consensus"> + <param name="sorting_method" value="RT_then_MZ"/> + <param name="sort_by_maps" value="true"/> + <param name="sort_by_size" value="true"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="TextExporter_1_input.featureXML"/> + <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="separator" value=""/> + <param name="replacement" value="_"/> + <param name="quoting" value="none"/> + <param name="no_ids" value="true"/> + <section name="feature"> + <param name="minimal" value="false"/> + <param name="add_metavalues" value="-1"/> + </section> + <section name="id"> + <param name="proteins_only" value="false"/> + <param name="peptides_only" value="false"/> + <param name="protein_groups" value="false"/> + <param name="first_dim_rt" value="false"/> + <param name="add_metavalues" value="-1"/> + <param name="add_hit_metavalues" value="-1"/> + <param name="add_protein_hit_metavalues" value="-1"/> + </section> + <section name="consensus"> + <param name="sorting_method" value="none"/> + <param name="sort_by_maps" value="false"/> + <param name="sort_by_size" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="TextExporter_9_input.idXML"/> + <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta="5700" ftype="tabular"/> + <param name="separator" value=""/> + <param name="replacement" value="_"/> + <param name="quoting" value="none"/> + <param name="no_ids" value="false"/> + <section name="feature"> + <param name="minimal" value="false"/> + <param name="add_metavalues" value="-1"/> + </section> + <section name="id"> + <param name="proteins_only" value="false"/> + <param name="peptides_only" value="false"/> + <param name="protein_groups" value="false"/> + <param name="first_dim_rt" value="false"/> + <param name="add_metavalues" value="0"/> + <param name="add_hit_metavalues" value="0"/> + <param name="add_protein_hit_metavalues" value="-1"/> + </section> + <section name="consensus"> + <param name="sorting_method" value="none"/> + <param name="sort_by_maps" value="false"/> + <param name="sort_by_size" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_TICCalculator"> + <test expect_num_outputs="1"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapNormalizer_output.mzML"/> + <param name="read_method" value="regular"/> + <param name="loadData" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapNormalizer_output.mzML"/> + <param name="read_method" value="streaming"/> + <param name="loadData" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapNormalizer_output.mzML"/> + <param name="read_method" value="streaming"/> + <param name="loadData" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapNormalizer_output.mzML"/> + <param name="read_method" value="indexed"/> + <param name="loadData" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MapNormalizer_output.mzML"/> + <param name="read_method" value="indexed_parallel"/> + <param name="loadData" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_TOFCalibration"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="TOFCalibration_1_input.mzML"/> + <output name="out" file="TOFCalibration_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/> + <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/> + <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/> + <param name="peak_data" value="false"/> + <section name="algorithm"> + <section name="PeakPicker"> + <param name="signal_to_noise" value="3.0"/> + <param name="centroid_percentage" value="0.6"/> + <param name="peak_width" value="0.15"/> + <param name="estimate_peak_width" value="false"/> + <param name="fwhm_lower_bound_factor" value="0.7"/> + <param name="fwhm_upper_bound_factor" value="20.0"/> + <section name="optimization"> + <param name="iterations" value="400"/> + <section name="penalties"> + <param name="position" value="0.0"/> + <param name="left_width" value="1.0"/> + <param name="right_width" value="1.0"/> + <param name="height" value="1.0"/> + </section> + <section name="2d"> + <param name="tolerance_mz" value="2.2"/> + <param name="max_peak_distance" value="1.2"/> + </section> + </section> + <section name="thresholds"> + <param name="peak_bound" value="400.0"/> + <param name="peak_bound_ms2_level" value="10.0"/> + <param name="correlation" value="0.0"/> + <param name="noise_level" value="0.1"/> + <param name="search_radius" value="3"/> + </section> + <section name="wavelet_transform"> + <param name="spacing" value="0.001"/> + </section> + <section name="deconvolution"> + <param name="deconvolution" value="false"/> + <param name="asym_threshold" value="0.3"/> + <param name="left_width" value="2.0"/> + <param name="right_width" value="2.0"/> + <param name="scaling" value="0.12"/> + <section name="fitting"> + <param name="fwhm_threshold" value="0.7"/> + <param name="eps_abs" value="9.999999747378752e-06"/> + <param name="eps_rel" value="9.999999747378752e-06"/> + <param name="max_iteration" value="10"/> + <section name="penalties"> + <param name="position" value="0.0"/> + <param name="height" value="1.0"/> + <param name="left_width" value="0.0"/> + <param name="right_width" value="0.0"/> + </section> + </section> + </section> + <section name="SignalToNoiseEstimationParameter"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="stdev_mp" value="3.0"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + </section> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="TOFCalibration_2_input.mzML"/> + <output name="out" file="TOFCalibration_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> + <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/> + <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/> + <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/> + <param name="peak_data" value="true"/> + <section name="algorithm"> + <section name="PeakPicker"> + <param name="signal_to_noise" value="3.0"/> + <param name="centroid_percentage" value="0.6"/> + <param name="peak_width" value="0.15"/> + <param name="estimate_peak_width" value="false"/> + <param name="fwhm_lower_bound_factor" value="0.7"/> + <param name="fwhm_upper_bound_factor" value="20.0"/> + <section name="optimization"> + <param name="iterations" value="400"/> + <section name="penalties"> + <param name="position" value="0.0"/> + <param name="left_width" value="1.0"/> + <param name="right_width" value="1.0"/> + <param name="height" value="1.0"/> + </section> + <section name="2d"> + <param name="tolerance_mz" value="2.2"/> + <param name="max_peak_distance" value="1.2"/> + </section> + </section> + <section name="thresholds"> + <param name="peak_bound" value="400.0"/> + <param name="peak_bound_ms2_level" value="10.0"/> + <param name="correlation" value="0.0"/> + <param name="noise_level" value="0.1"/> + <param name="search_radius" value="3"/> + </section> + <section name="wavelet_transform"> + <param name="spacing" value="0.001"/> + </section> + <section name="deconvolution"> + <param name="deconvolution" value="false"/> + <param name="asym_threshold" value="0.3"/> + <param name="left_width" value="2.0"/> + <param name="right_width" value="2.0"/> + <param name="scaling" value="0.12"/> + <section name="fitting"> + <param name="fwhm_threshold" value="0.7"/> + <param name="eps_abs" value="9.999999747378752e-06"/> + <param name="eps_rel" value="9.999999747378752e-06"/> + <param name="max_iteration" value="10"/> + <section name="penalties"> + <param name="position" value="0.0"/> + <param name="height" value="1.0"/> + <param name="left_width" value="0.0"/> + <param name="right_width" value="0.0"/> + </section> + </section> + </section> + <section name="SignalToNoiseEstimationParameter"> + <param name="max_intensity" value="-1"/> + <param name="auto_max_stdev_factor" value="3.0"/> + <param name="auto_max_percentile" value="95"/> + <param name="auto_mode" value="0"/> + <param name="win_len" value="200.0"/> + <param name="bin_count" value="30"/> + <param name="stdev_mp" value="3.0"/> + <param name="min_required_elements" value="10"/> + <param name="noise_for_empty_window" value="1e+20"/> + </section> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_TransformationEvaluation"> +</xml> + <xml name="autotest_XFDR"> + <test expect_num_outputs="4"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="XFDR_test_in1.idXML"/> + <output name="out_idXML" file="XFDR_test_out1_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <output name="out_mzIdentML" file="XFDR_test_out1_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> + <output name="out_xquest" file="XFDR_test_out1_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> + <param name="decoy_string" value="DECOY_"/> + <param name="minborder" value="-50.0"/> + <param name="maxborder" value="50.0"/> + <param name="mindeltas" value="0.0"/> + <param name="minionsmatched" value="0"/> + <param name="uniquexl" value="false"/> + <param name="no_qvalues" value="false"/> + <param name="minscore" value="-10.0"/> + <param name="binsize" value="0.1"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="4"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="XFDR_test_in1.idXML"/> + <output name="out_idXML" file="XFDR_test_out2_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <output name="out_mzIdentML" file="XFDR_test_out2_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> + <output name="out_xquest" file="XFDR_test_out2_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> + <param name="decoy_string" value="DECOY_"/> + <param name="minborder" value="-50.0"/> + <param name="maxborder" value="50.0"/> + <param name="mindeltas" value="0.0"/> + <param name="minionsmatched" value="0"/> + <param name="uniquexl" value="true"/> + <param name="no_qvalues" value="true"/> + <param name="minscore" value="-10.0"/> + <param name="binsize" value="0.1"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="4"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="XFDR_test_in2.xquest.xml"/> + <output name="out_idXML" file="XFDR_test_out3_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <output name="out_mzIdentML" file="XFDR_test_out3_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> + <output name="out_xquest" file="XFDR_test_out3_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> + <param name="decoy_string" value="DECOY_"/> + <param name="minborder" value="-50.0"/> + <param name="maxborder" value="50.0"/> + <param name="mindeltas" value="0.0"/> + <param name="minionsmatched" value="0"/> + <param name="uniquexl" value="false"/> + <param name="no_qvalues" value="false"/> + <param name="minscore" value="0.0"/> + <param name="binsize" value="0.1"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="4"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="XFDR_test_in2.xquest.xml"/> + <output name="out_idXML" file="XFDR_test_out4_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <output name="out_mzIdentML" file="XFDR_test_out4_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> + <output name="out_xquest" file="XFDR_test_out4_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> + <param name="decoy_string" value="DECOY_"/> + <param name="minborder" value="-3.0"/> + <param name="maxborder" value="3.0"/> + <param name="mindeltas" value="0.0"/> + <param name="minionsmatched" value="0"/> + <param name="uniquexl" value="false"/> + <param name="no_qvalues" value="false"/> + <param name="minscore" value="-10.0"/> + <param name="binsize" value="0.1"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="4"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="XFDR_test_in3.xquest.xml"/> + <output name="out_idXML" file="XFDR_test_out5_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <output name="out_mzIdentML" file="XFDR_test_out5_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> + <output name="out_xquest" file="XFDR_test_out5_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> + <param name="decoy_string" value="DECOY_"/> + <param name="minborder" value="-3.0"/> + <param name="maxborder" value="3.0"/> + <param name="mindeltas" value="0.0"/> + <param name="minionsmatched" value="0"/> + <param name="uniquexl" value="false"/> + <param name="no_qvalues" value="false"/> + <param name="minscore" value="-10.0"/> + <param name="binsize" value="0.1"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="XFDR_test_in4.idXML"/> + <output name="out_idXML" file="XFDR_test_out6_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="decoy_string" value="DECOY_"/> + <param name="minborder" value="-50.0"/> + <param name="maxborder" value="50.0"/> + <param name="mindeltas" value="0.0"/> + <param name="minionsmatched" value="0"/> + <param name="uniquexl" value="false"/> + <param name="no_qvalues" value="false"/> + <param name="minscore" value="-10.0"/> + <param name="binsize" value="0.1"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="4"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="XFDR_test_in2.xquest.xml"/> + <output name="out_idXML" file="XFDR_test_out7_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <output name="out_mzIdentML" file="XFDR_test_out7_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> + <output name="out_xquest" file="XFDR_test_out7_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> + <param name="decoy_string" value="DECOY_"/> + <param name="minborder" value="-50.0"/> + <param name="maxborder" value="50.0"/> + <param name="mindeltas" value="0.0"/> + <param name="minionsmatched" value="0"/> + <param name="uniquexl" value="true"/> + <param name="no_qvalues" value="false"/> + <param name="minscore" value="0.0"/> + <param name="binsize" value="0.1"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> + <xml name="autotest_XMLValidator"> +</xml> + <xml name="autotest_XTandemAdapter"> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="spectra.mzML"/> + <output name="out" file="XTandemAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="database" value="proteins.fasta"/> + <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/> + <param name="ignore_adapter_param" value="false"/> + <param name="precursor_mass_tolerance" value="5.0"/> + <param name="fragment_mass_tolerance" value="0.3"/> + <param name="precursor_error_units" value="ppm"/> + <param name="fragment_error_units" value="Da"/> + <param name="max_precursor_charge" value="0"/> + <param name="no_isotope_error" value="false"/> + <param name="fixed_modifications" value=""/> + <param name="variable_modifications" value="Oxidation (M)"/> + <param name="minimum_fragment_mz" value="150.0"/> + <param name="enzyme" value="Trypsin"/> + <param name="missed_cleavages" value="1"/> + <param name="semi_cleavage" value="false"/> + <param name="output_results" value="all"/> + <param name="max_valid_expect" value="0.1"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="spectra.mzML"/> + <output name="out" file="XTandemAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="database" value="proteins.fasta"/> + <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/> + <param name="ignore_adapter_param" value="false"/> + <param name="precursor_mass_tolerance" value="5.0"/> + <param name="fragment_mass_tolerance" value="0.3"/> + <param name="precursor_error_units" value="ppm"/> + <param name="fragment_error_units" value="Da"/> + <param name="max_precursor_charge" value="0"/> + <param name="no_isotope_error" value="false"/> + <param name="fixed_modifications" value=""/> + <param name="variable_modifications" value="Oxidation (M)"/> + <param name="minimum_fragment_mz" value="150.0"/> + <param name="enzyme" value="Trypsin"/> + <param name="missed_cleavages" value="1"/> + <param name="semi_cleavage" value="false"/> + <param name="output_results" value="valid"/> + <param name="max_valid_expect" value="1e-14"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="spectra.mzML"/> + <output name="out" file="XTandemAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="database" value="proteinslong.fasta"/> + <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/> + <param name="ignore_adapter_param" value="false"/> + <param name="precursor_mass_tolerance" value="5.0"/> + <param name="fragment_mass_tolerance" value="0.3"/> + <param name="precursor_error_units" value="ppm"/> + <param name="fragment_error_units" value="Da"/> + <param name="max_precursor_charge" value="0"/> + <param name="no_isotope_error" value="false"/> + <param name="fixed_modifications" value=""/> + <param name="variable_modifications" value="Oxidation (M)"/> + <param name="minimum_fragment_mz" value="150.0"/> + <param name="enzyme" value="Trypsin"/> + <param name="missed_cleavages" value="1"/> + <param name="semi_cleavage" value="false"/> + <param name="output_results" value="all"/> + <param name="max_valid_expect" value="0.1"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + </xml> +<xml name="autotest_PTPredict"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_RTPredict"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_InspectAdapter"/></macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_discarded_auto.xml Tue Oct 13 19:52:20 2020 +0000 @@ -0,0 +1,378 @@ + +<xml name="manutest_OpenSwathFileSplitter"> +<test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> + <output_collection name="outputDirectory" count=""/> + <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_qc_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> +</test></xml> +<xml name="manutest_IDRipper"> +<test expect_num_outputs="1"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDRipper_1_input.idXML"/> + <output_collection name="out_path" count=""/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test><test expect_num_outputs="1"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDRipper_2_input.idXML"/> + <output_collection name="out_path" count=""/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test><test expect_num_outputs="1"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDRipper_3_output.idXML"/> + <output_collection name="out_path" count=""/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test></xml> +<xml name="manutest_MzMLSplitter"> +<test expect_num_outputs="1"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_1_input.mzML"/> + <output_collection name="out" count=""/> + <param name="parts" value="2"/> + <param name="size" value="0"/> + <param name="unit" value="MB"/> + <param name="no_chrom" value="false"/> + <param name="no_spec" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test><test expect_num_outputs="1"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_1_input.mzML"/> + <output_collection name="out" count=""/> + <param name="parts" value="1"/> + <param name="size" value="40"/> + <param name="unit" value="KB"/> + <param name="no_chrom" value="false"/> + <param name="no_spec" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test></xml> +<xml name="manutest_MSFraggerAdapter"> +<test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="java_heapmemory" value="2600"/> + <param name="in" value="spectra.mzML"/> + <output name="out" file="MSFraggerAdapter_7_out_tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <output name="opt_out" file="MSFraggerAdapter_7_opt_out_tmp.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> + <param name="database" value="proteins.fasta"/> + <section name="tolerance"> + <param name="precursor_mass_tolerance" value="20.0"/> + <param name="precursor_mass_unit" value="ppm"/> + <param name="precursor_true_tolerance" value="0.0"/> + <param name="precursor_true_unit" value="ppm"/> + <param name="fragment_mass_tolerance" value="20.0"/> + <param name="fragment_mass_unit" value="ppm"/> + <param name="isotope_error" value="0"/> + </section> + <section name="digest"> + <param name="search_enzyme_name" value="Trypsin"/> + <param name="search_enzyme_cutafter" value="KR"/> + <param name="search_enzyme_nocutbefore" value="P"/> + <param name="num_enzyme_termini" value="semi"/> + <param name="allowed_missed_cleavage" value="2"/> + <param name="min_length" value="7"/> + <param name="max_length" value="64"/> + <param name="mass_range_min" value="500.0"/> + <param name="mass_range_max" value="5000.0"/> + </section> + <section name="varmod"> + <param name="clip_nterm_m" value="false"/> + <param name="masses" value=""/> + <param name="syntaxes" value=""/> + <param name="enable_common" value="true"/> + <param name="not_allow_multiple_variable_mods_on_residue" value="false"/> + <param name="max_variable_mods_per_mod" value="2"/> + <param name="max_variable_mods_combinations" value="5000"/> + </section> + <section name="spectrum"> + <param name="minimum_peaks" value="10"/> + <param name="use_topn_peaks" value="50"/> + <param name="minimum_ratio" value="0.0"/> + <param name="clear_mz_range_min" value="0.0"/> + <param name="clear_mz_range_max" value="0.0"/> + <param name="max_fragment_charge" value="2"/> + <param name="override_charge" value="false"/> + <param name="precursor_charge_min" value="1"/> + <param name="precursor_charge_max" value="4"/> + </section> + <section name="search"> + <param name="track_zero_topn" value="0"/> + <param name="zero_bin_accept_expect" value="0.0"/> + <param name="zero_bin_mult_expect" value="1.0"/> + <param name="add_topn_complementary" value="0"/> + <param name="min_fragments_modeling" value="3"/> + <param name="min_matched_fragments" value="4"/> + <param name="output_report_topn" value="1"/> + <param name="output_max_expect" value="50.0"/> + </section> + <section name="statmod"> + <param name="add_cterm_peptide" value="0.0"/> + <param name="add_nterm_peptide" value="0.0"/> + <param name="add_cterm_protein" value="0.0"/> + <param name="add_nterm_protein" value="0.0"/> + <param name="add_G_glycine" value="0.0"/> + <param name="add_A_alanine" value="0.0"/> + <param name="add_S_serine" value="0.0"/> + <param name="add_P_proline" value="0.0"/> + <param name="add_V_valine" value="0.0"/> + <param name="add_T_threonine" value="0.0"/> + <param name="add_C_cysteine" value="57.021464"/> + <param name="add_L_leucine" value="0.0"/> + <param name="add_I_isoleucine" value="0.0"/> + <param name="add_N_asparagine" value="0.0"/> + <param name="add_D_aspartic_acid" value="0.0"/> + <param name="add_Q_glutamine" value="0.0"/> + <param name="add_K_lysine" value="0.0"/> + <param name="add_E_glutamic_acid" value="0.0"/> + <param name="add_M_methionine" value="0.0"/> + <param name="add_H_histidine" value="0.0"/> + <param name="add_F_phenylalanine" value="0.0"/> + <param name="add_R_arginine" value="0.0"/> + <param name="add_Y_tyrosine" value="0.0"/> + <param name="add_W_tryptophan" value="0.0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,opt_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test><test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="java_heapmemory" value="2600"/> + <param name="in" value="spectra_comet.mzML"/> + <output name="out" file="MSFraggerAdapter_8_out_tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="database" value="proteins.fasta"/> + <section name="tolerance"> + <param name="precursor_mass_tolerance" value="20.0"/> + <param name="precursor_mass_unit" value="ppm"/> + <param name="precursor_true_tolerance" value="0.0"/> + <param name="precursor_true_unit" value="ppm"/> + <param name="fragment_mass_tolerance" value="20.0"/> + <param name="fragment_mass_unit" value="ppm"/> + <param name="isotope_error" value="0"/> + </section> + <section name="digest"> + <param name="search_enzyme_name" value="Trypsin"/> + <param name="search_enzyme_cutafter" value="KR"/> + <param name="search_enzyme_nocutbefore" value="P"/> + <param name="num_enzyme_termini" value="semi"/> + <param name="allowed_missed_cleavage" value="2"/> + <param name="min_length" value="7"/> + <param name="max_length" value="64"/> + <param name="mass_range_min" value="500.0"/> + <param name="mass_range_max" value="5000.0"/> + </section> + <section name="varmod"> + <param name="clip_nterm_m" value="false"/> + <param name="masses" value=""/> + <param name="syntaxes" value=""/> + <param name="enable_common" value="true"/> + <param name="not_allow_multiple_variable_mods_on_residue" value="false"/> + <param name="max_variable_mods_per_mod" value="2"/> + <param name="max_variable_mods_combinations" value="5000"/> + </section> + <section name="spectrum"> + <param name="minimum_peaks" value="10"/> + <param name="use_topn_peaks" value="50"/> + <param name="minimum_ratio" value="0.0"/> + <param name="clear_mz_range_min" value="0.0"/> + <param name="clear_mz_range_max" value="0.0"/> + <param name="max_fragment_charge" value="2"/> + <param name="override_charge" value="false"/> + <param name="precursor_charge_min" value="1"/> + <param name="precursor_charge_max" value="4"/> + </section> + <section name="search"> + <param name="track_zero_topn" value="0"/> + <param name="zero_bin_accept_expect" value="0.0"/> + <param name="zero_bin_mult_expect" value="1.0"/> + <param name="add_topn_complementary" value="0"/> + <param name="min_fragments_modeling" value="3"/> + <param name="min_matched_fragments" value="4"/> + <param name="output_report_topn" value="1"/> + <param name="output_max_expect" value="50.0"/> + </section> + <section name="statmod"> + <param name="add_cterm_peptide" value="0.0"/> + <param name="add_nterm_peptide" value="0.0"/> + <param name="add_cterm_protein" value="0.0"/> + <param name="add_nterm_protein" value="0.0"/> + <param name="add_G_glycine" value="0.0"/> + <param name="add_A_alanine" value="0.0"/> + <param name="add_S_serine" value="0.0"/> + <param name="add_P_proline" value="0.0"/> + <param name="add_V_valine" value="0.0"/> + <param name="add_T_threonine" value="0.0"/> + <param name="add_C_cysteine" value="57.021464"/> + <param name="add_L_leucine" value="0.0"/> + <param name="add_I_isoleucine" value="0.0"/> + <param name="add_N_asparagine" value="0.0"/> + <param name="add_D_aspartic_acid" value="0.0"/> + <param name="add_Q_glutamine" value="0.0"/> + <param name="add_K_lysine" value="0.0"/> + <param name="add_E_glutamic_acid" value="0.0"/> + <param name="add_M_methionine" value="0.0"/> + <param name="add_H_histidine" value="0.0"/> + <param name="add_F_phenylalanine" value="0.0"/> + <param name="add_R_arginine" value="0.0"/> + <param name="add_Y_tyrosine" value="0.0"/> + <param name="add_W_tryptophan" value="0.0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test></xml> +<xml name="manutest_MaRaClusterAdapter"> +<test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="verbose" value="2"/> + <param name="precursor_tolerance" value="20.0"/> + <param name="precursor_tolerance_units" value="ppm"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="MaRaClusterAdapter_1_in_1.mzML,MaRaClusterAdapter_1_in_2.mzML"/> + <param name="id_in" value="MaRaClusterAdapter_1_in_3.idXML"/> + <output name="out" file="MaRaClusterAdapter_2_out_1.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="pcut" value="-10.0"/> + <param name="min_cluster_size" value="1"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test></xml> +<xml name="manutest_NovorAdapter"> +<test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="NovorAdapter_in.mzML"/> + <output name="out" file="NovorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> + <param name="enzyme" value="Trypsin"/> + <param name="fragmentation" value="CID"/> + <param name="massAnalyzer" value="Trap"/> + <param name="fragment_mass_tolerance" value="0.5"/> + <param name="precursor_mass_tolerance" value="15.0"/> + <param name="precursor_error_units" value="ppm"/> + <param name="variable_modifications" value="Acetyl (K)"/> + <param name="fixed_modifications" value="Carbamidomethyl (C)"/> + <param name="forbiddenResidues" value="I"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test></xml> +<xml name="manutest_SpectraSTSearchAdapter"> +<test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="use_isotopically_averaged_mass" value="false"/> + <param name="use_all_charge_states" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/> + <param name="output_files_type" value="pep.xml"/> + <output_collection name="output_files" count="1"/> + <param name="library_file" value="testLib.splib" ftype="splib"/> + <param name="sequence_database_type" value="AA"/> + <param name="precursor_mz_tolerance" value="3.0"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test><test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="use_isotopically_averaged_mass" value="false"/> + <param name="use_all_charge_states" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/> + <param name="output_files_type" value="tsv"/> + <output_collection name="output_files" count="1"/> + <param name="library_file" value="testLib.splib" ftype="splib"/> + <param name="sequence_database_type" value="AA"/> + <param name="precursor_mz_tolerance" value="3.0"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test></xml>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_test.xml Tue Oct 13 19:52:20 2020 +0000 @@ -0,0 +1,545 @@ +<?xml version='1.0' encoding='UTF-8'?> +<macros> + +<!-- a copy of a FileConverter test without the advanced options used + in order to check if this works (all other tests enable advanced) --> +<xml name="manutest_FileConverter"> +<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> +</xml> +<!-- tests contributed by the galaxyproteomics community --> +<xml name="manutest_ClusterMassTracesByPrecursor"> + <test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in_ms1" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/> + <param name="in_swath" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/> + <output name="out" ftype="mzml" value="ClusterMassTracesByPrecursor.mzml"/> + </test> +</xml> +<xml name="manutest_ClusterMassTraces"> + <test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/> + <output name="out" ftype="mzml" value="ClusterMassTraces.mzml"/> + </test> +</xml> +<xml name="manutest_CVInspector"> + <!-- test with https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo listed here https://www.psidev.info/groups/controlled-vocabularies, mapping file from share/OpenMS/MAPPING/ms-mapping.xml, see currently not working, see: https://github.com/OpenMS/OpenMS/pull/4425 --> + <test expect_num_outputs="1"> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="cv_files" ftype="obo" value="CHEMISTRY/XLMOD.obo"/> + <param name="cv_names" value="XLMOD"/> + <param name="mapping_file" value="MAPPING/ms-mapping.xml"/> + <param name="OPTIONAL_OUTPUTS" value="html_FLAG"/> + <output name="html" ftype="html" value="CVInspector.html"/> + </test> +</xml> +<xml name="manutest_DeMeanderize"> + <test expect_num_outputs="1"><!-- test with the output of a MSsimulator output generated by a test below --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="mzml" value="MSsimulator_MALDI.mzml"/> + <output name="out" ftype="mzml" value="DeMeanderize.mzml"/> + </test> +</xml> +<xml name="manutest_Digestor"> + <test expect_num_outputs="1"><!-- just using some random fasta, in contrast to DigestorMotif idXML/fasta output possible, testing for the non-default fasta option --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="fasta" value="random.fa"/> + <output name="out" ftype="fasta" value="Digestor.fasta"/> + <param name="out_type" value="fasta"/> + </test> +</xml> +<xml name="manutest_EICExtractor"> + <test expect_num_outputs="1"><!-- just using some random test data --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" value="spectra.mzML"/> + <param name="pos" ftype="edta" value="FileConverter_10_input.edta"/> + <output name="out" ftype="csv" value="EICExtractor.csv" lines_diff="2"/> + </test> +</xml> +<xml name="manutest_ERPairFinder"> + <!-- TODO --> +</xml> +<xml name="manutest_FeatureFinderIsotopeWavelet"> + <test expect_num_outputs="1"><!--just use the input of another FeatureFinder --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" value="FeatureFinderCentroided_1_input.mzML"/> + <output name="out" value="FeatureFinderIsotopeWavelet.featureXML" compare="sim_size"/> + </test> +</xml> +<xml name="manutest_FFEval"> + <test expect_num_outputs="2"><!-- comparing an arbitarty FeatureFinder output with itself --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" value="FeatureFinderCentroided_1_output.featureXML"/> + <param name="truth" value="FeatureFinderCentroided_1_output.featureXML"/> + <param name="OPTIONAL_OUTPUTS" value="out_FLAG,out_roc_FLAG"/> + <output name="out" value="FFEval.featureXML" compare="sim_size"/> + <output name="out_roc" value="FFEval_roc.csv" ftype="csv"/> + </test> +</xml> +<xml name="manutest_IDExtractor"> + <test expect_num_outputs="1"><!-- --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/> + <param name="best_hits" value="true"/> + <param name="number_of_peptides" value="1"/> + <output name="out" value="IDExtractor.idXML" compare="sim_size"/> + </test> +</xml> +<!-- adapted from macros_discarded_auto.xml (due to prefix-output)--> +<xml name="manutest_IDRipper"> +<test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDRipper_1_input.idXML"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output_collection name="out_path" count="2"> + <element name="IDRipper_1_output_1" file="IDRipper_1_output1.idXML" ftype="idxml" compare="sim_size" delta="5700"/> + <element name="IDRipper_1_output_2" file="IDRipper_1_output2.idXML" ftype="idxml" compare="sim_size" delta="5700"/> + </output_collection> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> +</test> +<test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDRipper_2_input.idXML"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output_collection name="out_path" count="2"> + <element name="IDRipper_2_output1" file="IDRipper_2_output1.idXML" ftype="idxml"/> + <element name="IDRipper_2_output2" file="IDRipper_2_output2.idXML" ftype="idxml"/> + </output_collection> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> +</test> +<test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="IDRipper_3_output.idXML"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output_collection name="out_path" count="2"> + <element name="IDRipper_3_input1" file="IDRipper_3_input1.idXML" ftype="idxml"/> + <element name="IDRipper_3_input2" file="IDRipper_3_input2.idXML" ftype="idxml"/> + </output_collection> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> +</test> +</xml> +<xml name="manutest_LabeledEval"> + <test expect_num_outputs="1"><!-- comparing an arbitarty featureXML that has a corresponding consensusXML --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/> + <param name="truth" value="FeatureLinkerLabeled_1_output.consensusXML"/> + <output name="stdout" value="LabeledEval.txt" compare="sim_size"/> + </test> +</xml> +<xml name="manutest_MapStatistics"> + <test expect_num_outputs="1"><!-- test with a featureXML input --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="featurexml" value="SiriusAdapter_3_input.featureXML"/> + <output name="out" ftype="txt" value="MapStatistics.txt"/> + </test> + <test expect_num_outputs="1"><!-- test with a consensusxml input --> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="consensusxml" value="ConsensusXMLFile_1.consensusXML"/> + <output name="out" ftype="txt" value="MapStatistics2.txt"/> + </test> +</xml> +<xml name="manutest_MetaboliteSpectralMatcher"> + <!-- same input as used in the MSGF+Adapter, should use database CHEMISTRY/MetaboliteSpectralDB.mzML --> + <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter, used as input and database --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="mzml" value="spectra.mzML"/> + <param name="database" value="MetaboliteSpectralDB.mzML"/> + <output name="out" ftype="mztab" value="MetaboliteSpectralMatcher.mzTab"/> + </test> +</xml> +<xml name="manutest_MRMPairFinder"> + <!-- TODO no idea about a useful input for pair_in --> +</xml> +<xml name="manutest_MSSimulator"> + <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/> + <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/> + <output name="out" ftype="mzml" value="MSsimulator.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/> + <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/> + <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/> + </test> + <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter generate MALDI output for use in the test for DeMeanderize --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/> + <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/> + <output name="out" ftype="mzml" value="MSsimulator_MALDI.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/> + <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/> + <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/> + <param name="algorithm|MSSim|Global|ionization_type" value="MALDI"/> + </test> +</xml> +<!-- adapted from macros_discarded_auto.xml (due to prefix-output)--> +<xml name="manutest_MzMLSplitter"> +<test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_1_input.mzML"/> + <param name="parts" value="2"/> + <param name="size" value="0"/> + <param name="unit" value="MB"/> + <param name="no_chrom" value="false"/> + <param name="no_spec" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + <output_collection name="out" type="list" count="2"> + <element name="part1of2" file="MzMLSplitter_1_output_part1of2.mzML" ftype="mzml"/> + <element name="part2of2" file="MzMLSplitter_1_output_part2of2.mzML" ftype="mzml"/> + </output_collection> +</test> +<test expect_num_outputs="2"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="FileFilter_1_input.mzML"/> + <param name="parts" value="1"/> + <param name="size" value="40"/> + <param name="unit" value="KB"/> + <param name="no_chrom" value="false"/> + <param name="no_spec" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + <output_collection name="out" type="list" count="2"> + <element name="part1of2" file="MzMLSplitter_2_output_part1of2.mzML" ftype="mzml"/> + <element name="part2of2" file="MzMLSplitter_2_output_part2of2.mzML" ftype="mzml"/> + </output_collection> +</test> +</xml> +<xml name="manutest_OpenSwathDIAPreScoring"> + <!-- data from a test that included all the needed test files --> + <test> + <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> + <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> + <output_collection name="output_files" count="1"> + <element name="OpenSwathAnalyzer_2_swathfile_mzML.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/> + </output_collection> + </test> + + <!-- test with two inputs (actually the same file .. symlinked) --> + <test> + <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> + <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/> + <output_collection name="output_files" count="2"> + <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/> + <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/> + </output_collection> + </test> +</xml> +<!-- adapted from macros_discarded_auto.xml (due to prefix-output)--> +<xml name="manutest_OpenSwathFileSplitter"> + <test expect_num_outputs="3"> + <conditional name="adv_opts_cond"> + <param name="adv_opts_selector" value="advanced"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </conditional> + <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> + <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/> + <output_collection name="outputDirectory" count="6"> + <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/> + <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/> + </output_collection> + <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> +</xml> +<xml name="manutest_OpenSwathRewriteToFeatureXML"> + <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> + <param name="featureXML" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> + <param name="adv_opts_cond|test" value="true"/> + <output name="out" ftype="featurexml" value="OpenSwathRewriteToFeatureXML.featureXML"/> + </test> +</xml> +<xml name="manutest_PepNovoAdapter"> + <test expect_num_outputs="1"><!-- adapted from (dysfunctional) OMS 3rdParty tests (but model selection + unclear https://github.com/OpenMS/OpenMS/issues/4719)--> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="mzml" value="PepNovo_1.mzML"/> + <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/> + <param name="model" value="LTQ_COMP"/> + </test> + <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="mzml" value="PepNovo_1.mzML"/> + <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/> + <param name="model" value="LTQ_COMP"/> + </test> +</xml> +<xml name="manutest_PhosphoScoring"> + <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="mzml" value="spectra.mzML"/> + <param name="id" ftype="idxml" value="MSGFPlusAdapter_1_out1.tmp"/> + <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/> + </test> +</xml> +<xml name="manutest_PSMFeatureExtractor"> + <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible --> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/> + <param name="multiple_search_engines" value="true"/> + <param name="adv_opts_cond|adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|skip_db_check" value="true"/> + <param name="out_type" value="idxml"/> + <output name="out" ftype="idxml" value="PSMFeatureExtractor.idxml" compare="sim_size" delta="500"/> + </test> + <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible --> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/> + <param name="multiple_search_engines" value="true"/> + <param name="adv_opts_cond|adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|skip_db_check" value="true"/> + <param name="out_type" value="mzid"/> + <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="500"/> + </test> +</xml> +<xml name="manutest_QCCalculator"> + <test expect_num_outputs="1"><!-- took test data from another test w mzML input --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/> + <output name="out" ftype="qcml" value="QCCalculator1.qcML" compare="sim_size" delta="250"/> + </test> + <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,consensusXML input --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/> + <param name="id" ftype="idxml" value="OpenPepXL_output.idXML"/> + <param name="consensus" ftype="consensusxml" value="OpenPepXL_input.consensusXML"/> + <output name="out" ftype="qcml" value="QCCalculator2.qcML" compare="sim_size" delta="250"/> + </test> + <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,featureXML input --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="mzml" value="IDMapper_4_input.mzML"/> + <param name="id" ftype="idxml" value="IDMapper_4_input.idXML"/> + <param name="feature" ftype="featurexml" value="IDMapper_4_input.featureXML"/> + <output name="out" ftype="qcml" value="QCCalculator3.qcML" compare="sim_size" delta="250"/> + </test> +</xml> +<xml name="manutest_QCEmbedder"> + <!--TODO--> +</xml> +<xml name="manutest_QCExporter"> + <!--TODO--> +</xml> +<xml name="manutest_QCExtractor"> + <!--TODO--> +</xml> +<xml name="manutest_QCImporter"> + <!--TODO--> +</xml> +<xml name="manutest_QCMerger"> + <test expect_num_outputs="1"><!-- just using 2 outputs from QCCalculator as input (no2 did not work) --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="qcml" value="QCCalculator1.qcML,QCCalculator3.qcML"/> + <output name="out" ftype="qcml" value="QCMerger.qcML"/> + </test> +</xml> +<xml name="manutest_QCShrinker"> + <test expect_num_outputs="1"><!-- just using an output of QCCalculator as input --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="qcml" value="QCCalculator1.qcML"/> + <output name="out" ftype="qcml" value="QCShrinker.qcML"/> + </test> +</xml> +<xml name="manutest_RNADigestor"> + <test expect_num_outputs="1"><!--random RNAsequence input --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="fasta" value="random_RNA.fa"/> + <output name="out" ftype="fasta" value="RNADigestor.fasta"/> + </test> +</xml> +<xml name="manutest_RNPxlXICFilter"> + <test expect_num_outputs="1"><!-- just chosen an arbitrary input (2x the same which is likely nonsense, but sufficient for the test) and autgenerated output--> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="control" ftype="mzml" value="FileFilter_1_input.mzML"/> + <param name="treatment" ftype="mzml" value="FileFilter_1_input.mzML"/> + <output name="out" ftype="mzml" value="RNPxlXICFilter.mzML"/> + </test> +</xml> +<xml name="manutest_RTEvaluation"> + <!-- just chosen an arbitrary input and autgenerated output--> + <test expect_num_outputs="1"> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="idxml" value="PeptideIndexer_1.idXML"/> + <output name="out" ftype="tabular" value="RTEvaluation.tsv"/> + </test> +</xml> +<xml name="manutest_SemanticValidator"> + <test expect_num_outputs="1"><!-- just chosen an arbitrary input (same as XMLValidator) and autgenerated output--> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/> + <param name="mapping_file" ftype="xml" value="MAPPING/ms-mapping.xml"/> + <output name="stdout" ftype="txt" value="SemanticValidator.stdout" lines_diff="4"> + <assert_contents><has_text text="Congratulations, the file is valid!"/></assert_contents> + </output> + </test> +</xml> +<xml name="manutest_SequenceCoverageCalculator"> + <test expect_num_outputs="1"><!-- took test data from another tool that also takes idXML and fasta as input --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in_database" value="PeptideIndexer_1.fasta" ftype="fasta"/> + <param name="in_peptides" value="SequenceCoverageCalculator_1.idXML" ftype="idxml"/> + <output name="out" value="SequenceCoverageCalculator.txt" ftype="txt" compare="sim_size"/> + </test> +</xml> +<xml name="manutest_SpecLibCreator"> + <!--TODO could not find test data --> +</xml> +<xml name="manutest_SpectraFilterBernNorm"> + <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> + <output name="out" value="SpectraFilterBernNorm.mzML" compare="sim_size"/> + </test> +</xml> +<xml name="manutest_SpectraFilterMarkerMower"> + <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> + <output name="out" value="SpectraFilterMarkerMower.mzML" compare="sim_size"/> + </test> +</xml> +<xml name="manutest_SpectraFilterNLargest"> + <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> + <output name="out" value="SpectraFilterNLargest.mzML" compare="sim_size"/> + </test> +</xml> +<xml name="manutest_SpectraFilterNormalizer"> + <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> + <output name="out" value="SpectraFilterNormalizer.mzML" compare="sim_size"/> + </test> +</xml> +<xml name="manutest_SpectraFilterParentPeakMower"> + <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> + <output name="out" value="SpectraFilterParentPeakMower.mzML" compare="sim_size"/> + </test> +</xml> +<xml name="manutest_SpectraFilterScaler"> + <test expect_num_outputs="1"> <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> + <output name="out" value="SpectraFilterScaler.mzML" compare="sim_size"/> + </test> +</xml> +<xml name="manutest_SpectraFilterThresholdMower"> + <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> + <output name="out" value="SpectraFilterThresholdMower.mzML" compare="sim_size"/> + </test> +</xml> +<xml name="manutest_SpectraMerger"> + <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output--> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="mzml" value="NovorAdapter_in.mzML"/> + <output name="out" ftype="mzml" value="SpectraMerger_1.mzML" compare="sim_size"/> + </test> +</xml> +<xml name="manutest_SvmTheoreticalSpectrumGeneratorTrainer"> +<!-- -TODO model_output_file creates multiple files--> +</xml> +<xml name="manutest_TransformationEvaluation"> + <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output--> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="trafoxml" value="FileInfo_16_input.trafoXML"/> + <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/> + <output name="out" ftype="trafoxml" value="TransformationEvaluation.trafoXML" compare="sim_size" delta="100000000"/> + </test> +</xml> +<xml name="manutest_XMLValidator"> + <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output--> + <param name="adv_opts_selector" value="advanced"/> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/> + <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4"> + <assert_contents><has_text text="Success: the file is valid!"/></assert_contents> + </output> + </test> +</xml> +<xml name="manutest_MetaboliteAdductDecharger"/><xml name="manutest_IDMapper"/><xml name="manutest_ProteinQuantifier"/><xml name="manutest_PeakPickerIterative"/><xml name="manutest_FeatureLinkerUnlabeledQT"/><xml name="manutest_TICCalculator"/><xml name="manutest_IDFilter"/><xml name="manutest_IDPosteriorErrorProbability"/><xml name="manutest_FeatureFinderIdentification"/><xml name="manutest_XFDR"/><xml name="manutest_OpenSwathWorkflow"/><xml name="manutest_MassCalculator"/><xml name="manutest_IDFileConverter"/><xml name="manutest_MultiplexResolver"/><xml name="manutest_FeatureFinderSuperHirn"/><xml name="manutest_AssayGeneratorMetabo"/><xml name="manutest_MassTraceExtractor"/><xml name="manutest_SiriusAdapter"/><xml name="manutest_IDMerger"/><xml name="manutest_MSstatsConverter"/><xml name="manutest_FileMerger"/><xml name="manutest_Decharger"/><xml name="manutest_PTPredict"/><xml name="manutest_XTandemAdapter"/><xml name="manutest_FeatureFinderMetabo"/><xml name="manutest_CruxAdapter"/><xml name="manutest_OpenSwathConfidenceScoring"/><xml name="manutest_PrecursorIonSelector"/><xml name="manutest_ConsensusMapNormalizer"/><xml name="manutest_RTPredict"/><xml name="manutest_PercolatorAdapter"/><xml name="manutest_ProteinInference"/><xml name="manutest_OpenSwathDecoyGenerator"/><xml name="manutest_TextExporter"/><xml name="manutest_FeatureFinderCentroided"/><xml name="manutest_DecoyDatabase"/><xml name="manutest_SpectraFilterWindowMower"/><xml name="manutest_NoiseFilterGaussian"/><xml name="manutest_MaRaClusterAdapter"/><xml name="manutest_ConsensusID"/><xml name="manutest_FileFilter"/><xml name="manutest_InclusionExclusionListCreator"/><xml name="manutest_FeatureLinkerUnlabeledKD"/><xml name="manutest_NovorAdapter"/><xml name="manutest_OpenPepXL"/><xml name="manutest_SeedListGenerator"/><xml name="manutest_FalseDiscoveryRate"/><xml name="manutest_OpenPepXLLF"/><xml name="manutest_SpecLibSearcher"/><xml name="manutest_IDConflictResolver"/><xml name="manutest_MRMMapper"/><xml name="manutest_OMSSAAdapter"/><xml name="manutest_ExternalCalibration"/><xml name="manutest_PeakPickerHiRes"/><xml name="manutest_MascotAdapter"/><xml name="manutest_FeatureFinderMultiplex"/><xml name="manutest_MetaProSIP"/><xml name="manutest_FuzzyDiff"/><xml name="manutest_TargetedFileConverter"/><xml name="manutest_MapAlignerIdentification"/><xml name="manutest_IDRTCalibration"/><xml name="manutest_MRMTransitionGroupPicker"/><xml name="manutest_RTModel"/><xml name="manutest_OpenSwathAssayGenerator"/><xml name="manutest_IDSplitter"/><xml name="manutest_OpenSwathMzMLFileCacher"/><xml name="manutest_HighResPrecursorMassCorrector"/><xml name="manutest_OpenSwathChromatogramExtractor"/><xml name="manutest_OpenSwathAnalyzer"/><xml name="manutest_FeatureLinkerUnlabeled"/><xml name="manutest_CompNovoCID"/><xml name="manutest_DTAExtractor"/><xml name="manutest_FileInfo"/><xml name="manutest_MapAlignerSpectrum"/><xml name="manutest_IsobaricAnalyzer"/><xml name="manutest_LowMemPeakPickerHiRes"/><xml name="manutest_MyriMatchAdapter"/><xml name="manutest_InternalCalibration"/><xml name="manutest_TOFCalibration"/><xml name="manutest_MSGFPlusAdapter"/><xml name="manutest_PTModel"/><xml name="manutest_InspectAdapter"/><xml name="manutest_SpectraFilterSqrtMower"/><xml name="manutest_SimpleSearchEngine"/><xml name="manutest_PeakPickerWavelet"/><xml name="manutest_MapNormalizer"/><xml name="manutest_IDScoreSwitcher"/><xml name="manutest_FeatureLinkerLabeled"/><xml name="manutest_MapRTTransformer"/><xml name="manutest_RNPxlSearch"/><xml name="manutest_PrecursorMassCorrector"/><xml name="manutest_MapAlignerPoseClustering"/><xml name="manutest_MzTabExporter"/><xml name="manutest_BaselineFilter"/><xml name="manutest_FeatureFinderMRM"/><xml name="manutest_MascotAdapterOnline"/><xml name="manutest_DatabaseFilter"/><xml name="manutest_ProteinResolver"/><xml name="manutest_OpenSwathFeatureXMLToTSV"/><xml name="manutest_FidoAdapter"/><xml name="manutest_AccurateMassSearch"/><xml name="manutest_CompNovo"/><xml name="manutest_LowMemPeakPickerHiResRandomAccess"/><xml name="manutest_OpenSwathRTNormalizer"/><xml name="manutest_PeptideIndexer"/><xml name="manutest_CometAdapter"/><xml name="manutest_NoiseFilterSGolay"/><xml name="manutest_MSFraggerAdapter"/><xml name="manutest_SpectraSTSearchAdapter"/><xml name="manutest_SequestAdapter"/><xml name="manutest_FeatureFinder"/><xml name="manutest_LuciphorAdapter"/><xml name="manutest_GNPSExport"/><xml name="manutest_Epifany"/><xml name="manutest_NucleicAcidSearchEngine"/><xml name="manutest_QualityControl"/><xml name="manutest_FeatureFinderMetaboIdent"/><xml name="manutest_RNAMassCalculator"/><xml name="manutest_MapAlignerTreeGuided"/><xml name="manutest_IDMassAccuracy"/><xml name="manutest_ProteomicsLFQ"/><xml name="manutest_IDDecoyProbability"/><xml name="manutest_DigestorMotif"/><xml name="manutest_DatabaseSuitability"/><xml name="manutest_StaticModification"/></macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/prepare_test_data_manual.sh Tue Oct 13 19:52:20 2020 +0000 @@ -0,0 +1,161 @@ +MSSimulator -test -in DecoyDatabase_1.fasta -out MSsimulator.mzml -algorithm:RandomNumberGenerators:biological reproducible -algorithm:RandomNumberGenerators:technical reproducible > MSSimulator_1.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'MSSimulator_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +MSSimulator -test -in DecoyDatabase_1.fasta -out MSsimulator_MALDI.mzml -algorithm:RandomNumberGenerators:biological reproducible -algorithm:RandomNumberGenerators:technical reproducible -algorithm:MSSim:Global:ionization_type MALDI > MSSimulator_2.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'MSSimulator_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +ClusterMassTracesByPrecursor -test -in_ms1 ConsensusMapNormalizer_input.consensusXML -in_swath ConsensusMapNormalizer_input.consensusXML -out ClusterMassTracesByPrecursor.mzml > ClusterMassTracesByPrecursor.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'ClusterMassTracesByPrecursor failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +ClusterMassTraces -test -in ConsensusMapNormalizer_input.consensusXML -out ClusterMassTraces.mzml > ClusterMassTraces.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'ClusterMassTraces failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +CVInspector -test -cv_files CHEMISTRY/XLMOD.obo -cv_names XLMOD -mapping_file MAPPING/ms-mapping.xml -html CVInspector.html > CVInspector.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'CVInspector failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +DeMeanderize -test -in MSsimulator_MALDI.mzml -out DeMeanderize.mzml > DeMeanderize.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'DeMeanderize failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +# TODO DigestorMotif + +Digestor -test -in random.fa -out Digestor.fasta -out_type fasta > Digestor.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'Digestor failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +EICExtractor -test -in spectra.mzML -pos FileConverter_10_input.edta -out EICExtractor.csv > EICExtractor.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'EICExtractor failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +#TODO ERPairFinder + +FeatureFinderIsotopeWavelet -test -in FeatureFinderCentroided_1_input.mzML -out FeatureFinderIsotopeWavelet.featureXML > FeatureFinderIsotopeWavelet.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'FeatureFinderIsotopeWavelet failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + + +FFEval -test -in FeatureFinderCentroided_1_output.featureXML -truth FeatureFinderCentroided_1_output.featureXML -out FFEval.featureXML -out_roc FFEval_roc.csv > FFEval.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'FFEval failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +# TODO? deprecated IDDecoyProbability + +IDExtractor -test -in MSGFPlusAdapter_1_out.idXML -best_hits -number_of_peptides 1 -out IDExtractor.idXML > IDExtractor.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'IDExtractor failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +LabeledEval -test -in FeatureLinkerLabeled_1_input.featureXML -truth FeatureLinkerLabeled_1_output.consensusXML> LabeledEval.txt > LabeledEval.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'LabeledEval failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +MapStatistics -test -in SiriusAdapter_3_input.featureXML -out MapStatistics.txt > MapStatistics_1.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'MapStatistics_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +MapStatistics -test -in ConsensusXMLFile_1.consensusXML -out MapStatistics2.txt > MapStatistics_2.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'MapStatistics_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +MetaboliteAdductDecharger -test -in Decharger_input.featureXML -out_cm MetaboliteAdductDecharger_cm.consensusXML -out_fm MetaboliteAdductDecharger_fm.featureXML -outpairs MetaboliteAdductDecharger_pairs.consensusXML > MetaboliteAdductDecharger.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'MetaboliteAdductDecharger failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +MetaboliteSpectralMatcher -test -in spectra.mzML -database MetaboliteSpectralDB.mzML -out MetaboliteSpectralMatcher.mzTab > MetaboliteSpectralMatcher.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'MetaboliteSpectralMatcher failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +# TODO MRMPairFinder + +# generate two inputs for OpenSwathDIAPreScoring +OpenSwathDIAPreScoring -tr OpenSwathWorkflow_1_input.TraML -swath_files OpenSwathAnalyzer_2_swathfile.mzML -output_files OpenSwathDIAPreScoring.tsv > OpenSwathDIAPreScoring.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'OpenSwathDIAPreScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +# generate two inputs for OpenSwathDIAPreScoring by linking +ln -s OpenSwathAnalyzer_2_swathfile.mzML OpenSwathDIAPreScoring_in1.mzML +ln -s OpenSwathAnalyzer_2_swathfile.mzML OpenSwathDIAPreScoring_in2.mzML +OpenSwathDIAPreScoring -tr OpenSwathWorkflow_1_input.TraML -swath_files OpenSwathDIAPreScoring_in1.mzML OpenSwathDIAPreScoring_in2.mzML -output_files OpenSwathDIAPreScoring_2_1.tsv OpenSwathDIAPreScoring_2_2.tsv > OpenSwathDIAPreScoring.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'OpenSwathDIAPreScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +OpenSwathRewriteToFeatureXML -featureXML OpenSwathFeatureXMLToTSV_input.featureXML -out OpenSwathRewriteToFeatureXML.featureXML > OpenSwathRewriteToFeatureXML.stdout 2> stderr +# if [[ "$?" -ne "0" ]]; then >&2 echo 'OpenSwathRewriteToFeatureXML failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +# adapted from the commented tests in OpenMS TODO may be removed later https://github.com/OpenMS/OpenMS/issues/4719 +FileConverter -in PepNovo.mzXML -out PepNovo_1.mzML > /dev/null 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'FileConverter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +PepNovoAdapter -ini PepNovoAdapter_1_parameters.ini -in PepNovo_1.mzML -out PepNovoAdapter_3_output.idXML -model_directory pepnovo_models/ -pepnovo_executable pepnovo > PepNovo_1.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +FileConverter -in PepNovo.mzData -out PepNovo_4.mzML > /dev/null 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'FileConverter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi +PepNovoAdapter -ini PepNovoAdapter_1_parameters.ini -in PepNovo_4.mzML -out PepNovoAdapter_4_output.idXML -model_directory pepnovo_models/ -pepnovo_executable pepnovo > PepNovo_1.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +#PepNovoAdapter -ini PepNovoAdapter_5_parameters.ini -in PepNovoAdapter_5_output.pepnovo_out -out PepNovoAdapter_5_output.idXML -model_directory pepnovo_models/ + +# TODO PhosphoScoring +PhosphoScoring -in spectra.mzML -id MSGFPlusAdapter_1_out1.tmp -out PhosphoScoring.idxml > PhosphoScoring.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out PSMFeatureExtractor.idxml > PSMFeatureExtractor_1.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi +PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out PSMFeatureExtractor.mzid > PSMFeatureExtractor_2.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +QCCalculator -test -in OpenPepXL_input.mzML -out QCCalculator1.qcML > QCCalculator_1.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'QCCalculator_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi +QCCalculator -test -in OpenPepXL_input.mzML -id OpenPepXL_output.idXML -consensus OpenPepXL_input.consensusXML -out QCCalculator2.qcML > QCCalculator_2.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'QCCalculator_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi +QCCalculator -test -in IDMapper_4_input.mzML -id IDMapper_4_input.idXML -feature IDMapper_4_input.featureXML -out QCCalculator3.qcML > QCCalculator_3.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'QCCalculator_3 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +# TODO QCEmbedder +# TODO QCExporter +# TODO QCExtractor +# TODO QCImporter + +QCMerger -test -in QCCalculator1.qcML QCCalculator3.qcML -out QCMerger.qcML > QCMerger.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'QCMerger failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +QCShrinker -test -in QCCalculator1.qcML -out QCShrinker.qcML > QCShrinker.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'QCShrinker failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +RNADigestor -test -in random_RNA.fa -out RNADigestor.fasta > RNADigestor.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'RNADigestor failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +RNPxlXICFilter -test -control FileFilter_1_input.mzML -treatment FileFilter_1_input.mzML -out RNPxlXICFilter.mzML > RNPxlXICFilter.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'RNPxlXICFilter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +RTEvaluation -in PeptideIndexer_1.idXML -out RTEvaluation.tsv > RTEvaluation.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'RTEvaluation failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +SemanticValidator -test -in FileFilter_1_input.mzML -mapping_file MAPPING/ms-mapping.xml > SemanticValidator.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'SemanticValidator failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +IDFilter -in PeptideIndexer_1.idXML -best:strict -out SequenceCoverageCalculator_1.idXML > IDFilter.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'IDFilter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi +SequenceCoverageCalculator -test -in_database PeptideIndexer_1.fasta -in_peptides SequenceCoverageCalculator_1.idXML -out SequenceCoverageCalculator.txt > SequenceCoverageCalculator.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'SequenceCoverageCalculator failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +# TODO SpecLibCreator + +SpectraFilterBernNorm -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterBernNorm.mzML > SpectraFilterBernNorm.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraFilterBernNorm failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +SpectraFilterMarkerMower -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterMarkerMower.mzML > SpectraFilterMarkerMower.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraFilterMarkerMower failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +SpectraFilterNLargest -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterNLargest.mzML > SpectraFilterNLargest.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraFilterNLargest failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +SpectraFilterNormalizer -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterNormalizer.mzML > SpectraFilterNormalizer.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraFilterNormalizer failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +SpectraFilterParentPeakMower -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterParentPeakMower.mzML > SpectraFilterParentPeakMower.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraFilterParentPeakMower failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +SpectraFilterScaler -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterScaler.mzML > SpectraFilterScaler.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraFilterScaler failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +SpectraFilterThresholdMower -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterThresholdMower.mzML > SpectraFilterThresholdMower.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraFilterThresholdMower failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +SpectraMerger -test -in NovorAdapter_in.mzML -out SpectraMerger_1.mzML > SpectraMerger.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraMerger failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +# TODO SvmTheoreticalSpectrumGeneratorTrainer + +TransformationEvaluation -test -in FileInfo_16_input.trafoXML -out TransformationEvaluation.trafoXML > TransformationEvaluation.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'TransformationEvaluation failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi + +XMLValidator -test -in FileFilter_1_input.mzML > XMLValidator.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'XMLValidator failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi
--- a/readme.md Fri May 17 10:22:48 2019 -0400 +++ b/readme.md Tue Oct 13 19:52:20 2020 +0000 @@ -8,175 +8,127 @@ More informations are available at: * https://github.com/OpenMS/OpenMS - * http://open-ms.sourceforge.net + * https://www.openms.de/ + +The wrappers for these tools and most of their tests are automatically +generated using the `generate.sh` script. The generation of the tools is +based on the CTDConverter (https://github.com/WorkflowConversion/CTDConverter) +which can be fine tuned via the `hardcoded_params.json` file. This file allows +to blacklist and hardcode parameters and to modify or set arbitrary +CTD/XML attributes. + +Note that, due to its size, the test data is excluded from this repository. In +order to generate the test data on call `test-data.sh`. + +Manual updates should only be done to + +- the `@GALAXY_VERSION@"` token in `macros.xml` +- and the manually contributed tests in `macros_test.xml` (The goal is that all + tools that do not have an automatically generated test are covered here) +- the `hardcoded_params.json` files + +In a few cases patches may be acceptable. + +Installation +============ + +The Galaxy OpenMS tools can be installed from the toolshed. While most tools +will work out of the box some need attention since requirements can not be +fulfilled via Conda: + +Not yet in Conda are: + +- SpectraST (http://tools.proteomecenter.org/wiki/index.php?title=SpectraST) +- MaRaCluster (https://github.com/statisticalbiotechnology/maracluster) + +Binaries for these tools can easily be obtained via: + +``` +VERSION=.... +git git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git OpenMS$VERSION.0-git +git submodule init OpenMS$VERSION.0-git +git submodule update OpenMS$VERSION.0-git +``` + +They are located in `OpenMS$VERSION-git/THIRDPARTY/`. +Not in Conda due to licencing restrictions: + +- Mascot http://www.matrixscience.com/ +- MSFragger https://github.com/Nesvilab/MSFragger +- Novor http://www.rapidnovor.org/novor + +There are multiple ways to enable the Galaxy tools to use these binaries. + +- Just copy them to the `bin` path within Galaxy's conda environment +- Put them in any other path that that is included in PATH +- Edit the corresponding tools: In the command line part search for the parameters `-executable`, `-maracluster_executable`, or `-mascot_directory` and edit them appropriately. + +Working +======= + +The tools work by: + +Preprocessing: + +- For each input / output data set parameter a directory is crated (named by + the parameter) +- For input data set parameters the links to the actual location of the data + sets are created + +Main: + +- The galaxy wrapper create two json config files: one containing the + parameters and the values chosen by the user and the other the values of + hardcoded parameters. +- With `OpenMSTool -write_ctd ./` a CTD (names OpenMSTool.ctd) file is + generated that contains the default values. +- A call to `fill_ctd.py` fills in the values from the json config files into + the CTD file +- The actual tool is called `OpenMSTool -ini OpenMSTool.ctd` and also all input + and output parameters are given on the command line. + +Postprocessing: + +- output data sets are moved to the final locations + +Note: The reason for handling data sets on the command line (and not specifying +them in the CTD file) is mainly that all files in Galaxy have the extension +`.dat` and OpenMS tools require an appropriate extension. But this may change +in the future. Generating OpenMS wrappers ========================== - * install OpenMS (you can do this automatically through Conda) - * create a folder called CTD - * if you installed openms as a binary in a specific directory, execute the following command in the `openms/bin` directory: - - ```bash - for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done; - ``` - - * if there is no binary release (e.g. as with version 2.2), download and unpack the Conda package, find the `bin` folder and create a list of the tools as follow: - - ```bash - ls >> tools.txt - ``` - - * search for the `bin` folder of your conda environment containing OpenMS and do: - - ```bash - while read p; do - ./PATH/TO/BIN/$p -write_ctd /PATH/TO/YOUR/CTD; - done <tools.txt - ``` - - * You should have all CTD files now. `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`). +1. remove old test data: `rm -rf $(ls -d test-data/* | egrep -v "random|\.loc")` +2. `./generate.sh` - * clone or install CTDopts - - ```bash - git clone https://github.com/genericworkflownodes/CTDopts - ``` - - * add CTDopts to your `$PYTHONPATH` - - ```bash - export PYTHONPATH=/home/user/CTDopts/ - ``` - - * clone or install CTD2Galaxy +Whats happening: - ```bash - git clone https://github.com/WorkflowConversion/CTDConverter.git - ``` - - * If you have CTDopts and CTDConverter installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it. Further information can be found on the CTDConverter page. +1. The binaries of the OpenMS package can generate a CTD file that describes + the parameters. These CTD files are converted to xml Galaxy tool descriptions + using the `CTDConverter`. - ```bash - python convert.py galaxy \ - -i /PATH/TO/YOUR/CTD/*.ctd \ - -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \ - -d datatypes_conf.xml -g openms \ - -b version log debug test no_progress threads \ - in_type executable myrimatch_executable \ - fido_executable fidocp_executable \ - omssa_executable pepnovo_e xecutable \ - xtandem_executable param_model_directory \ - java_executable java_memory java_permgen \ - r_executable rt_concat_trafo_out param_id_pool \ - -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \ - -s PATH/TO/tools_blacklist.txt - ``` - - - * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. Some of these tools might already be deprecated and the files might not exist: - - ``` - sed -i '13 a\-fido_executable Fido' wrappers/FidoAdapter.xml - sed -i '13 a\-fidocp_executable FidoChooseParameters' wrappers/FidoAdapter.xml - sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml - sed -i '13 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml - sed -i '13 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml - ``` - - * For some tools, additional work has to be done. In `MSGFPlusAdapter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where): - - ``` - <command><![CDATA[ - - ## check input file type - #set $in_type = $param_in.ext +2. The CI testing framework of OpenMS contains command lines and test data + (https://github.com/OpenMS/OpenMS/tree/develop/src/tests/topp). These tests + are described in two CMake files. - ## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files - ln -s '$param_in' 'param_in.${in_type}' && - ln -s '$param_database' param_database.fasta && - ## find location of the MSGFPlus.jar file of the msgf_plus conda package - MSGF_JAR=\$(msgf_plus -get_jar_path) && + - From these CMake files Galaxy tests are auto generated and stored in `macros_autotest.xml` + - The command lines are stored in `prepare_test_data.sh` for regeneration of test data + +More details can be found in the comments of the shell script. + +Open problems +============= - MSGFPlusAdapter - -executable \$MSGF_JAR - #if $param_in: - -in 'param_in.${in_type}' - #end if - #if $param_out: - -out $param_out - #end if - #if $param_mzid_out: - -mzid_out $param_mzid_out - #end if - #if $param_database: - -database param_database.fasta - #end if - - [...] - ]]> - ``` - - * In Xtandem Converter and probably in others: - - ``` - #if str($param_missed_cleavages) != '': - ``` - This is because integers needs to be compared as string otherwise `0` becomes `false`. - - * In `MetaProSIP.xml` add `R` as a requirement: - - ``` - <expand macro="requirements"> - <requirement type="package" version="3.3.1">r-base</requirement> - </expand> - ``` - - * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where): - - ``` - <command><![CDATA[ - - ## check input file type - #set $in_type = $param_in.ext +Some tools stall in CI testing using `--biocontainers` which is why the OpenMS +tools are currently listed in `.tt_biocontainer_skip`. This is - ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files - ln -s '$param_in' 'param_in.${in_type}' && - - IDFileConverter - - #if $param_in: - -in 'param_in.${in_type}' - #end if - - [...] - ]]> - ``` +- AssayGeneratorMetabo and SiriusAdapter (both depend on sirius) +- OMSSAAdapter - * In `IDFileConverter.xml` and `FileConverter.xml` add `auto_format="true"` to the output, e.g.: - - - `<data name="param_out" auto_format="true"/>` - - `<data name="param_out" metadata_source="param_in" auto_format="true"/>` - - * To add an example test case to `DecoyDatabase.xml` add the following after the output section. If standard settings change you might have to adjust the options and/or the test files. - - ``` - <tests> - <test> - <param name="param_in" value="DecoyDatabase_input.fasta"/> - <output name="param_out" file="DecoyDatabase_output.fasta"/> - </test> - </tests> - ``` - - * Additionally cause of lacking dependencies, the following adapters have been removed in `SKIP_TOOLS_FILES.txt` as well: - * OMSSAAdapter - * MyrimatchAdapter - - * Additionally cause of a problematic parameter (-model_directory), the following adapter has been removed: - * PepNovoAdapter - +Using `docker -t` seems to solve the problem (see +https://github.com/galaxyproject/galaxy/issues/10153). Licence (MIT) =============
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data.sh Tue Oct 13 19:52:20 2020 +0000 @@ -0,0 +1,265 @@ +#!/usr/bin/env bash + +VERSION=2.6 +FILETYPES="filetypes.txt" +CONDAPKG="https://anaconda.org/bioconda/openms/2.6.0/download/linux-64/openms-2.6.0-h4afb90d_0.tar.bz2" + +# import the magic +. ./generate-foo.sh + +# install conda +if [ -z "$tmp" ]; then + tmp=$(mktemp -d) + created="yes" +fi + +export OPENMSGIT="$tmp/OpenMS$VERSION.0-git" +export OPENMSPKG="$tmp/OpenMS$VERSION-pkg/" +export OPENMSENV="$tmp/OpenMS$VERSION-env" +export CTDCONVERTER="$tmp/CTDConverter" + +if [[ -z "$1" ]]; then + autotests="/dev/null" +else + autotests="$1" +fi + +if type conda > /dev/null; then + true +else + wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh + bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda" + source "$tmp/miniconda/bin/activate" +fi +eval "$(conda shell.bash hook)" + + +############################################################################### +## get +## - conda environment (for executing the binaries) and +## - the git clone of OpenMS (for generating the tests) +############################################################################### + +echo "Clone OpenMS $VERSION sources" +if [[ ! -d $OPENMSGIT ]]; then + git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT + cd $OPENMSGIT + git submodule init + git submodule update + cd - +else + cd $OPENMSGIT + git pull origin release/$VERSION.0 + cd - +fi + +echo "Create OpenMS $VERSION conda env" +# TODO currently add lxml (needed by CTDConverter) +# TODO for some reason a to recent openjdk is used +if conda env list | grep "$OPENMSENV"; then + true +else + conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -p $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION ctdopts=1.4 lxml +# chmod -R u-w $OPENMSENV +fi +############################################################################### +## get the +## - conda package (for easy access and listing of the OpenMS binaries), +############################################################################### +echo "Download OpenMS $VERSION package $CONDAPKG" + +if [[ ! -d $OPENMSPKG ]]; then + mkdir $OPENMSPKG + wget -q -P $OPENMSPKG/ "$CONDAPKG" + tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C $OPENMSPKG/ + rm $OPENMSPKG/"$(basename $CONDAPKG)" +fi + +############################################################################### +## Get python libaries for CTD -> Galaxy conversion +## TODO fix to main repo OR conda packkage if PRs are merged +############################################################################### +echo "Clone CTDConverter" +if [[ ! -d $CTDCONVERTER ]]; then + #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter + git clone -b topic/cdata https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER +else + cd $CTDCONVERTER + git pull origin topic/cdata + cd - +fi + +############################################################################### +## copy all the test data files to test-data +## most of it (outputs) will be overwritten later, but its needed for +## prepare_test_data +############################################################################### +echo "Get test data" +find test-data -type f,l,d ! -name "*fa" ! -name "*loc" -delete + +cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/ +cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/ +cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/ +cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/ +if [[ ! -f test-data/MetaboliteSpectralDB.mzML ]]; then + wget -nc https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML + mv MetaboliteSpectralDB.mzML test-data/ +fi +ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt +ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv + +if [ ! -d test-data/pepnovo_models/ ]; then + mkdir -p /tmp/pepnovo + wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip + unzip PepNovo.20120423.zip -d /tmp/pepnovo/ + mv /tmp/pepnovo/Models test-data/pepnovo_models/ + rm PepNovo.20120423.zip + rm -rf /tmp/pepnovo +fi +############################################################################### +## generate ctd files using the binaries in the conda package +############################################################################### +echo "Create CTD files" +conda activate $OPENMSENV +rm -rf ctd +mkdir -p ctd + +# TODO because of https://github.com/OpenMS/OpenMS/issues/4641 +# this needs to be done from within test-data +cd test-data +for i in $OPENMSPKG/bin/* +do + b=$(basename $i) + echo $b + $b -write_ctd ../ctd/ + sed -i -e 's/²/^2/' ../ctd/$b.ctd +done +cd - +############################################################################### +## fix ini files: OpenMS test data contains ini files with outdated ini files. +## e.g. variables might be in different nodes, outdated variables present, new +## variables missing, ... +## OpenMS tools fix this on the fly (so its no problem for the OpenMS tests) +## but it is for the generation of the tests +## see https://github.com/OpenMS/OpenMS/issues/4462 +############################################################################### +echo "Update test INI files" +for ini in test-data/*ini +do + tool=$(cat $ini | grep 'NODE name="' | head -n 1 | sed 's/.*name="\([^"]\+\)".*/\1/') + bin=$(which $tool) + if [[ -z $bin ]]; then + >&2 echo "missing binary to convert $ini" + continue + fi + cp $ini $ini.backup + $bin -ini $ini -write_ini $ini > $ini.stdout 2> $ini.stderr + if [[ "$?" -ne "0" ]]; then + >&2 echo "could not convert $ini" + fi +done + +############################################################################### +## create script to create results for the tests and run it +############################################################################### +echo "Create test shell script" + +echo -n "" > prepare_test_data.sh +echo 'export COMET_BINARY="comet"' >> prepare_test_data.sh +echo 'export CRUX_BINARY="crux"' >> prepare_test_data.sh +echo 'export FIDOCHOOSEPARAMS_BINARY="FidoChooseParameters"' >> prepare_test_data.sh +echo 'export FIDO_BINARY="Fido"' >> prepare_test_data.sh +echo 'export LUCIPHOR_BINARY="$(dirname $(realpath $(which luciphor2)))/luciphor2.jar"' >> prepare_test_data.sh + +echo 'export MARACLUSTER_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster"'>> prepare_test_data.sh +echo 'export MSFRAGGER_BINARY="/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar"'>> prepare_test_data.sh +echo 'export MSGFPLUS_BINARY="$(msgf_plus -get_jar_path)"' >> prepare_test_data.sh +echo 'export MYRIMATCH_BINARY="myrimatch"'>> prepare_test_data.sh +echo 'export NOVOR_BINARY="/home/berntm/Downloads/novor/lib/novor.jar"' >> prepare_test_data.sh +echo 'export OMSSA_BINARY="$(dirname $(realpath $(which omssacl)))/omssacl"'>> prepare_test_data.sh +echo 'export PERCOLATOR_BINARY="percolator"'>> prepare_test_data.sh +echo 'export SIRIUS_BINARY="$(which sirius)"' >> prepare_test_data.sh +echo 'export SPECTRAST_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/SpectraST/spectrast"' >> prepare_test_data.sh +echo 'export XTANDEM_BINARY="xtandem"' >> prepare_test_data.sh +echo 'export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"' >> prepare_test_data.sh + +prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh + +# prepare_test_data > tmp_test_data.sh +# # remove calls not needed for the tools listed in any .list file +# echo LIST $LIST +# if [ ! -z "$LIST" ]; then +# REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//') +# else +# REX=".*" +# fi +# echo REX $REX +# cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh +# rm tmp_test_data.sh + +echo "Execute test shell script" +chmod u+x prepare_test_data.sh +cd ./test-data || exit +../prepare_test_data.sh +cd - || exit + + +############################################################################### +## create/update test data for the manually generated tests +## - run convert once with the manual tests only and +## - update test-data (needs to run 2x) +############################################################################### +echo "Execute test shell script for manually curated tests" +chmod u+x prepare_test_data_manual.sh + +cd ./test-data || exit +../prepare_test_data_manual.sh +cd - || exit + + +############################################################################### +## auto generate tests +############################################################################### +echo "Write test macros to $autotests" +echo "<macros>" > "$autotests" +for i in $(ls *xml |grep -v macros) +do + b=$(basename "$i" .xml) + get_tests2 "$b" >> "$autotests" +done +echo "</macros>" >> "$autotests" + +echo "Create test data links" +link_tmp_files + +# tests for tools using output_prefix parameters can not be auto generated +# hence we output the tests for manual curation in macros_test.xml +# and remove them from the autotests +# -> OpenSwathFileSplitter IDRipper MzMLSplitter +# +# Furthermore we remove tests for tools without binaries in conda +# -> MSFragger MaRaClusterAdapter NovorAdapter +# +# not able to specify composite test data +# -> SpectraSTSearchAdapter +if [[ ! -z "$1" ]]; then + echo "" > macros_discarded_auto.xml + for i in OpenSwathFileSplitter IDRipper MzMLSplitter MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter + do + echo "<xml name=\"manutest_$i\">" >> macros_discarded_auto.xml + xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >> macros_discarded_auto.xml + echo "</xml>" >> macros_discarded_auto.xml + xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp + mv tmp macros_autotest.xml + done + >&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml" +fi +conda deactivate + +## remove broken symlinks in test-data +find test-data/ -xtype l -delete + +# if [ ! -z "$created" ]; then +# echo "Removing temporary directory" +# rm -rf "$tmp" +# fi
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/pepnovo_models.loc.sample Tue Oct 13 19:52:20 2020 +0000 @@ -0,0 +1,23 @@ +# This is a sample file distributed with Galaxy that enables tools +# to use pepnovo models +# The file has three tab separated columns: name, value, and path. +# The idea is that there are a number of models in a directory: +# - each model directory has a unique name (columns 2 and 0) +# - each model can contain a set of models (column 1) +# +# The following example works fo the default models from +# http://proteomics.ucsd.edu/Software/PepNovo.html (just remove the comment +# chars and replace DIR_TO_PEPNOVO_MODELS) + +#default_models CID_IT_TRYP DIR_TO_PEPNOVO_MODELS +#default_models LTQ_COMP DIR_TO_PEPNOVO_MODELS +#default_models DBC4_PEAK DIR_TO_PEPNOVO_MODELS +#default_models CID_IT_TRYP_TAG5 DIR_TO_PEPNOVO_MODELS +#default_models CID_IT_TRYP_TAG6 DIR_TO_PEPNOVO_MODELS +#default_models ITDNV_PEAK DIR_TO_PEPNOVO_MODELS +#default_models CID_IT_TRYP_SCORE DIR_TO_PEPNOVO_MODELS +#default_models CID_IT_TRYP_TAG3 DIR_TO_PEPNOVO_MODELS +#default_models CID_IT_TRYP_DNVPART DIR_TO_PEPNOVO_MODELS +#default_models CID_IT_TRYP_TAG4 DIR_TO_PEPNOVO_MODELS +#default_models CID_IT_TRYP_DB DIR_TO_PEPNOVO_MODELS +#default_models CID_IT_TRYP_CSP DIR_TO_PEPNOVO_MODELS
--- a/tool.conf Fri May 17 10:22:48 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,160 +0,0 @@ -<?xml version='1.0' encoding='UTF-8'?> -<toolbox> - <section id="section-id-Peptidepropertyprediction" name="Peptide property prediction"> - <tool file="openms/PTModel.xml"/> - <tool file="openms/PTPredict.xml"/> - <tool file="openms/RTModel.xml"/> - <tool file="openms/RTPredict.xml"/> - </section> - <section id="section-id-TargetedExperiments" name="Targeted Experiments"> - <tool file="openms/InclusionExclusionListCreator.xml"/> - <tool file="openms/MRMMapper.xml"/> - <tool file="openms/OpenSwathAnalyzer.xml"/> - <tool file="openms/OpenSwathAssayGenerator.xml"/> - <tool file="openms/OpenSwathChromatogramExtractor.xml"/> - <tool file="openms/OpenSwathConfidenceScoring.xml"/> - <tool file="openms/OpenSwathDecoyGenerator.xml"/> - <tool file="openms/OpenSwathDIAPreScoring.xml"/> - <tool file="openms/OpenSwathFeatureXMLToTSV.xml"/> - <tool file="openms/OpenSwathFileSplitter.xml"/> - <tool file="openms/OpenSwathMzMLFileCacher.xml"/> - <tool file="openms/OpenSwathRewriteToFeatureXML.xml"/> - <tool file="openms/OpenSwathRTNormalizer.xml"/> - <tool file="openms/PrecursorIonSelector.xml"/> - <tool file="openms/TargetedFileConverter.xml"/> - </section> - <section id="section-id-Utilities" name="Utilities"> - <tool file="openms/AccurateMassSearch.xml"/> - <tool file="openms/CVInspector.xml"/> - <tool file="openms/DatabaseFilter.xml"/> - <tool file="openms/DecoyDatabase.xml"/> - <tool file="openms/DeMeanderize.xml"/> - <tool file="openms/Digestor.xml"/> - <tool file="openms/DigestorMotif.xml"/> - <tool file="openms/ERPairFinder.xml"/> - <tool file="openms/FFEval.xml"/> - <tool file="openms/FuzzyDiff.xml"/> - <tool file="openms/IDDecoyProbability.xml"/> - <tool file="openms/IDExtractor.xml"/> - <tool file="openms/IDMassAccuracy.xml"/> - <tool file="openms/IDScoreSwitcher.xml"/> - <tool file="openms/IDSplitter.xml"/> - <tool file="openms/LabeledEval.xml"/> - <tool file="openms/LowMemPeakPickerHiRes.xml"/> - <tool file="openms/LowMemPeakPickerHiRes_RandomAccess.xml"/> - <tool file="openms/MassCalculator.xml"/> - <tool file="openms/MetaboliteSpectralMatcher.xml"/> - <tool file="openms/MetaProSIP.xml"/> - <tool file="openms/MRMPairFinder.xml"/> - <tool file="openms/MRMTransitionGroupPicker.xml"/> - <tool file="openms/MSSimulator.xml"/> - <tool file="openms/MultiplexResolver.xml"/> - <tool file="openms/MzMLSplitter.xml"/> - <tool file="openms/OpenSwathWorkflow.xml"/> - <tool file="openms/QCCalculator.xml"/> - <tool file="openms/QCEmbedder.xml"/> - <tool file="openms/QCExporter.xml"/> - <tool file="openms/QCExtractor.xml"/> - <tool file="openms/QCImporter.xml"/> - <tool file="openms/QCMerger.xml"/> - <tool file="openms/QCShrinker.xml"/> - <tool file="openms/RNPxl.xml"/> - <tool file="openms/RNPxlSearch.xml"/> - <tool file="openms/RNPxlXICFilter.xml"/> - <tool file="openms/RTEvaluation.xml"/> - <tool file="openms/SemanticValidator.xml"/> - <tool file="openms/SequenceCoverageCalculator.xml"/> - <tool file="openms/SimpleSearchEngine.xml"/> - <tool file="openms/SpecLibCreator.xml"/> - <tool file="openms/SpectraSTSearchAdapter.xml"/> - <tool file="openms/SvmTheoreticalSpectrumGeneratorTrainer.xml"/> - <tool file="openms/TICCalculator.xml"/> - <tool file="openms/TopPerc.xml"/> - <tool file="openms/TransformationEvaluation.xml"/> - <tool file="openms/XMLValidator.xml"/> - </section> - <section id="section-id-MapAlignment" name="Map Alignment"> - <tool file="openms/ConsensusMapNormalizer.xml"/> - <tool file="openms/FeatureLinkerLabeled.xml"/> - <tool file="openms/FeatureLinkerUnlabeled.xml"/> - <tool file="openms/FeatureLinkerUnlabeledKD.xml"/> - <tool file="openms/FeatureLinkerUnlabeledQT.xml"/> - <tool file="openms/MapRTTransformer.xml"/> - </section> - <section id="section-id-IDProcessing" name="ID Processing"> - <tool file="openms/ConsensusID.xml"/> - <tool file="openms/FalseDiscoveryRate.xml"/> - <tool file="openms/FidoAdapter.xml"/> - <tool file="openms/IDConflictResolver.xml"/> - <tool file="openms/IDFileConverter.xml"/> - <tool file="openms/IDFilter.xml"/> - <tool file="openms/IDMapper.xml"/> - <tool file="openms/IDPosteriorErrorProbability.xml"/> - <tool file="openms/IDRTCalibration.xml"/> - <tool file="openms/LuciphorAdapter.xml"/> - <tool file="openms/PeptideIndexer.xml"/> - <tool file="openms/PhosphoScoring.xml"/> - </section> - <section id="section-id-Signalprocessingandpreprocessing" name="Signal processing and preprocessing"> - <tool file="openms/BaselineFilter.xml"/> - <tool file="openms/ExternalCalibration.xml"/> - <tool file="openms/HighResPrecursorMassCorrector.xml"/> - <tool file="openms/InternalCalibration.xml"/> - <tool file="openms/MapNormalizer.xml"/> - <tool file="openms/MassTraceExtractor.xml"/> - <tool file="openms/NoiseFilterGaussian.xml"/> - <tool file="openms/NoiseFilterSGolay.xml"/> - <tool file="openms/PeakPickerHiRes.xml"/> - <tool file="openms/PeakPickerIterative.xml"/> - <tool file="openms/PeakPickerWavelet.xml"/> - <tool file="openms/PrecursorMassCorrector.xml"/> - <tool file="openms/SpectraMerger.xml"/> - <tool file="openms/TOFCalibration.xml"/> - </section> - <section id="section-id-Identification" name="Identification"> - <tool file="openms/CompNovoCID.xml"/> - <tool file="openms/CompNovo.xml"/> - <tool file="openms/InspectAdapter.xml"/> - <tool file="openms/MascotAdapter.xml"/> - <tool file="openms/MascotAdapterOnline.xml"/> - <tool file="openms/MSGFPlusAdapter.xml"/> - <tool file="openms/ProteinInference.xml"/> - <tool file="openms/SpectraFilterBernNorm.xml"/> - <tool file="openms/SpectraFilterMarkerMower.xml"/> - <tool file="openms/SpectraFilterNLargest.xml"/> - <tool file="openms/SpectraFilterNormalizer.xml"/> - <tool file="openms/SpectraFilterParentPeakMower.xml"/> - <tool file="openms/SpectraFilterScaler.xml"/> - <tool file="openms/SpectraFilterSqrtMower.xml"/> - <tool file="openms/SpectraFilterThresholdMower.xml"/> - <tool file="openms/SpectraFilterWindowMower.xml"/> - <tool file="openms/XTandemAdapter.xml"/> - </section> - <section id="section-id-FileHandling" name="File Handling"> - <tool file="openms/DTAExtractor.xml"/> - <tool file="openms/FileConverter.xml"/> - <tool file="openms/FileFilter.xml"/> - <tool file="openms/FileInfo.xml"/> - <tool file="openms/FileMerger.xml"/> - <tool file="openms/IDMerger.xml"/> - <tool file="openms/IDRipper.xml"/> - <tool file="openms/MapStatistics.xml"/> - <tool file="openms/MzTabExporter.xml"/> - <tool file="openms/TextExporter.xml"/> - </section> - <section id="section-id-Quantitation" name="Quantitation"> - <tool file="openms/AdditiveSeries.xml"/> - <tool file="openms/Decharger.xml"/> - <tool file="openms/EICExtractor.xml"/> - <tool file="openms/FeatureFinderCentroided.xml"/> - <tool file="openms/FeatureFinderIdentification.xml"/> - <tool file="openms/FeatureFinderIsotopeWavelet.xml"/> - <tool file="openms/FeatureFinderMetabo.xml"/> - <tool file="openms/FeatureFinderMRM.xml"/> - <tool file="openms/FeatureFinderMultiplex.xml"/> - <tool file="openms/FeatureFinderSuperHirn.xml"/> - <tool file="openms/IsobaricAnalyzer.xml"/> - <tool file="openms/ProteinQuantifier.xml"/> - <tool file="openms/ProteinResolver.xml"/> - </section> -</toolbox>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Oct 13 19:52:20 2020 +0000 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of pepnovo models --> + <table name="pepnovo_models" comment_char="#" allow_duplicate_entries="False"> + <columns>name,value,path</columns> + <file path="tool-data/pepnovo_models.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Oct 13 19:52:20 2020 +0000 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all eggnog_mapper data --> + <table name="pepnovo_models" comment_char="#"> + <columns>name,value,path</columns> + <file path="${__HERE__}/test-data/pepnovo_models.loc" /> + </table> +</tables>
--- a/tools_blacklist.txt Fri May 17 10:22:48 2019 -0400 +++ b/tools_blacklist.txt Tue Oct 13 19:52:20 2020 +0000 @@ -1,9 +1,21 @@ -OMSSAAdapter -MyriMatchAdapter -PepNovoAdapter -SeedListGenerator -SpecLibSearcher -MapAlignerIdentification -MapAlignerPoseClustering -MapAlignerSpectrum -MapAlignerRTTransformer +# seems not possible for 2.5 https://github.com/OpenMS/OpenMS/issues/4426 +# DigestorMotif + +# deprecated https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/UTILS_IDDecoyProbability.html +# https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/a16242.html +IDDecoyProbability + +# personal communication with author V. Bafna: +# "InsPect is no longer maintained as there are many better tools including MS-GF+" +InspectAdapter + +# licence? see https://github.com/bioconda/bioconda-recipes/issues/18953 +#MSFraggerAdapter + +# https://github.com/OpenMS/OpenMS/issues/4550#issuecomment-594065727 +ProteomicsLFQ + +# https://github.com/OpenMS/OpenMS/issues/4401 +InclusionExclusionListCreator +RTPredict +PTPredict