Mercurial > repos > galaxyp > openms_databasesuitability
changeset 0:d994c72a91fc draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
| author | galaxyp |
|---|---|
| date | Tue, 13 Oct 2020 19:54:23 +0000 |
| parents | |
| children | 594a165c069c |
| files | 404-urls.patch DatabaseSuitability.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_data_table_conf.xml.sample tool_data_table_conf.xml.test tools_blacklist.txt |
| diffstat | 21 files changed, 29903 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/404-urls.patch Tue Oct 13 19:54:23 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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/DatabaseSuitability.xml Tue Oct 13 19:54:23 2020 +0000 @@ -0,0 +1,99 @@ +<?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: []--> +<tool id="DatabaseSuitability" name="DatabaseSuitability" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> + <description>Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra.</description> + <macros> + <token name="@EXECUTABLE@">DatabaseSuitability</token> + <import>macros.xml</import> + <import>macros_autotest.xml</import> + <import>macros_test.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re + +## Preprocessing +mkdir in_id && +ln -s '$in_id' 'in_id/${re.sub("[^\w\-_]", "_", $in_id.element_identifier)}.$gxy2omsext($in_id.ext)' && +mkdir in_spec && +ln -s '$in_spec' 'in_spec/${re.sub("[^\w\-_]", "_", $in_spec.element_identifier)}.$gxy2omsext($in_spec.ext)' && +mkdir in_novo && +ln -s '$in_novo' 'in_novo/${re.sub("[^\w\-_]", "_", $in_novo.element_identifier)}.$gxy2omsext($in_novo.ext)' && +#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + mkdir out && +#end if + +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd +-in_id +'in_id/${re.sub("[^\w\-_]", "_", $in_id.element_identifier)}.$gxy2omsext($in_id.ext)' +-in_spec +'in_spec/${re.sub("[^\w\-_]", "_", $in_spec.element_identifier)}.$gxy2omsext($in_spec.ext)' +-in_novo +'in_novo/${re.sub("[^\w\-_]", "_", $in_novo.element_identifier)}.$gxy2omsext($in_novo.ext)' +#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + -out + 'out/output.${gxy2omsext("tabular")}' +#end if +#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 + | tee '$stdout' +#end if + +## Postprocessing +#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + && mv 'out/output.${gxy2omsext("tabular")}' '$out' +#end if +#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="in_id" argument="-in_id" type="data" format="idxml" optional="false" label="Input idXML file from peptide search with combined database with added de novo peptide" help="PeptideIndexer is needed, FDR is forbidden select idxml data sets(s)"/> + <param name="in_spec" argument="-in_spec" type="data" format="mzml" optional="false" label="Input MzML file used for the peptide identification" help=" select mzml data sets(s)"/> + <param name="in_novo" argument="-in_novo" type="data" format="idxml" optional="false" label="Input idXML file containing de novo peptides (unfiltered)" help=" select idxml data sets(s)"/> + <section name="algorithm" title="Parameter section for the suitability calculation algorithm" help="" expanded="false"> + <param name="no_rerank" argument="-algorithm:no_rerank" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag if you want to disable re-ranking" help="Cases, where a de novo peptide scores just higher than the database peptide, are overlooked and counted as a de novo hit. This might underestimate the database quality"/> + <param name="reranking_cutoff_percentile" argument="-algorithm:reranking_cutoff_percentile" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Swap a top-scoring deNovo hit with a lower scoring DB hit if their xcorr score difference is in the given percentile of all score differences between the first two decoy hits of a PSM" help="The lower the value the lower the decoy cut-off will be. Therefore it will be harder for a lower scoring DB hit to be re-ranked to the top"/> + <param name="FDR" argument="-algorithm:FDR" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Filter peptide hits based on this q-value" help="(e.g., 0.05 = 5 % FDR)"/> + </section> + <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="out_FLAG">out (Optional tsv output containing database suitability information as well as spectral quality)</option> + <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> + </param> + </inputs> + <outputs> + <data name="out" label="${tool.name} on ${on_string}: out" format="tabular"> + <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> + <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> + <filter>OPTIONAL_OUTPUTS is None</filter> + </data> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> + </outputs> + <tests> + <expand macro="autotest_DatabaseSuitability"/> + <expand macro="manutest_DatabaseSuitability"/> + </tests> + <help><![CDATA[Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra. + +]]></help> + <expand macro="references"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OMSSAAdapter.patch Tue Oct 13 19:54:23 2020 +0000 @@ -0,0 +1,10 @@ +--- OMSSAAdapter.xml 2020-06-16 15:51:40.315400730 +0200 ++++ /tmp/OMSSAAdapter.xml 2020-06-16 15:50:23.536086074 +0200 +@@ -22,6 +22,7 @@ + mkdir database && + ln -s '$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 19:54:23 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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filetypes.txt Tue Oct 13 19:54:23 2020 +0000 @@ -0,0 +1,85 @@ +# 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 19:54:23 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 19:54:23 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 19:54:23 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 $test_id.stdout)\";fi" + done +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate.sh Tue Oct 13 19:54:23 2020 +0000 @@ -0,0 +1,76 @@ +#!/usr/bin/env bash + +VERSION=2.6 +FILETYPES="filetypes.txt" +PROFILE="20.05" +## FILETYPES_RE=$(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 $i.json & +# done
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hardcoded_params.json Tue Oct 13 19:54:23 2020 +0000 @@ -0,0 +1,236 @@ +{ + "#": "blacklist parameters", + + "version": [{"value": "@"}], + "debug": [{"value": "@"}], + "algorithm:debug": [{"value": "@"}], + "java_memory": [{"value": "@"}], + "java_permgen": [{"value": "@"}], + "#": "type of input is always determined from the file extension ", + "in_type": [{"value": "@"}], + + "#": "tool specific blacklist parameters", + + "convert_back": [{"value": "@", "tools": ["OpenSwathMzMLFileCacher"]}], + "NET_executable": [{ + "value": "@", + "tools": ["FileConverter"] + }], + + + "params_file": [{"value": "@", "tools": ["SpectraSTSearchAdapter"]}], + + "#": "TODO not usable in 2.5 https://github.com/OpenMS/OpenMS/issues/4456, corresponding test currently disabled", + "consensus_out": [{"value": "@", "tools": ["MaRaClusterAdapter"]}], + "#": "TODO would need treatment as prefix-output", + "output_directory": [{"value": "@", "tools": ["MaRaClusterAdapter"]}], + + "#": "hardcode parameter values", + + "comet_version": [{ + "value":"2016.01 rev. 3" + }], + "comet_executable": [{ + "value":"comet" + }], + "crux_executable": [{ + "value": "crux" + }], + "fido_executable": [{ + "value":"Fido" + }], + "fidocp_executable": [{ + "value":"FidoChooseParameters" + }], + "maracluster_executable": [{ + "value":"/home/berntm/projects/tools-galaxyp/tools/openms/OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster" + }], + "mascot_directory": [{ + "value":"TODO" + }], + "myrimatch_executable": [{ + "value":"myrimatch" + }], + "omssa_executable": [{ + "value":"$(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"] + + }] +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Oct 13 19:54:23 2020 +0000 @@ -0,0 +1,128 @@ +<?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="@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> + <xml name="stdio"> + <stdio> + <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/> + <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/> + <regex match="qUncompress: could not allocate enough memory to uncompress data" level="fatal_oom" description="Java memory Exception"/> + </stdio> + </xml> + <xml name="references"> + <citations> + <citation type="doi">doi:10.1186/1471-2105-9-163</citation> + </citations> + </xml> + <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> + </param> + <when value="basic"/> + <when value="advanced"> + <yield/> + </when> + </conditional> + </xml> + + <!-- 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 19:54:23 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 19:54:23 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 19:54:23 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 19:54:23 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.md Tue Oct 13 19:54:23 2020 +0000 @@ -0,0 +1,153 @@ +Galaxy wrapper for OpenMS +========================= + +OpenMS is an open-source software C++ library for LC/MS data management and analyses. +It offers an infrastructure for the rapid development of mass spectrometry related software. +OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux. + +More informations are available at: + + * https://github.com/OpenMS/OpenMS + * 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 +========================== + +1. remove old test data: `rm -rf $(ls -d test-data/* | egrep -v "random|\.loc")` +2. `./generate.sh` + +Whats happening: + +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`. + +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. + + - 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 +============= + +Some tools stall in CI testing using `--biocontainers` which is why the OpenMS +tools are currently listed in `.tt_biocontainer_skip`. This is + +- AssayGeneratorMetabo and SiriusAdapter (both depend on sirius) +- OMSSAAdapter + +Using `docker -t` seems to solve the problem (see +https://github.com/galaxyproject/galaxy/issues/10153). + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data.sh Tue Oct 13 19:54:23 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 19:54:23 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Oct 13 19:54:23 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 19:54:23 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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools_blacklist.txt Tue Oct 13 19:54:23 2020 +0000 @@ -0,0 +1,21 @@ +# 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