# HG changeset patch
# User galaxyp
# Date 1599681860 0
# Node ID 8fad84d1a74d033eeb1b1c737952d98af1767bfa
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
diff -r 000000000000 -r 8fad84d1a74d ClusterMassTraces.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ClusterMassTraces.xml Wed Sep 09 20:04:20 2020 +0000
@@ -0,0 +1,74 @@
+
+
+
+
+ Creates pseudo spectra.
+
+ ClusterMassTraces
+ macros.xml
+ macros_autotest.xml
+ macros_test.xml
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+ OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS
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+
diff -r 000000000000 -r 8fad84d1a74d OMSSAAdapter.patch
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OMSSAAdapter.patch Wed Sep 09 20:04:20 2020 +0000
@@ -0,0 +1,10 @@
+--- OMSSAAdapter.xml 2020-06-16 15:51:40.315400730 +0200
++++ /tmp/OMSSAAdapter.xml 2020-06-16 15:50:23.536086074 +0200
+@@ -22,6 +22,7 @@
+ mkdir database &&
+ ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
+
++makeblastdb -dbtype prot -in 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
+ ## Main program call
+
+ set -o pipefail &&
diff -r 000000000000 -r 8fad84d1a74d PepNovoAdapter.patch
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/PepNovoAdapter.patch Wed Sep 09 20:04:20 2020 +0000
@@ -0,0 +1,35 @@
+--- PepNovoAdapter.xml 2020-05-12 15:55:24.712831518 +0200
++++ /tmp/PepNovoAdapter.xml 2020-05-12 15:36:31.267276757 +0200
+@@ -42,8 +42,13 @@
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+@@ -51,8 +56,14 @@
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diff -r 000000000000 -r 8fad84d1a74d filetypes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/filetypes.txt Wed Sep 09 20:04:20 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
+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
diff -r 000000000000 -r 8fad84d1a74d fill_ctd.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fill_ctd.py Wed Sep 09 20:04:20 2020 +0000
@@ -0,0 +1,190 @@
+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
+# - 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
+ # 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, lineage, 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.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)
diff -r 000000000000 -r 8fad84d1a74d fill_ctd_clargs.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fill_ctd_clargs.py Wed Sep 09 20:04:20 2020 +0000
@@ -0,0 +1,40 @@
+#!/usr/bin/env python3
+from argparse import ArgumentParser
+from io import StringIO
+
+from CTDopts.CTDopts import (
+ CTDModel,
+ ModelTypeError,
+ Parameters
+)
+
+if __name__ == "__main__":
+ # note add_help=False since otherwise arguments starting with -h will
+ # trigger an error (despite allow_abbreviate)
+ parser = ArgumentParser(prog="fill_ctd_clargs",
+ description="fill command line arguments"
+ "into a CTD file and write the CTD file to",
+ add_help=False, allow_abbrev=False)
+ parser.add_argument("--ctd", dest="ctd", help="input ctd file",
+ metavar='CTD', default=None, required=True)
+ args, cliargs = parser.parse_known_args()
+ # load CTDModel
+ model = None
+ try:
+ model = CTDModel(from_file=args.ctd)
+ except ModelTypeError:
+ pass
+ try:
+ model = Parameters(from_file=args.ctd)
+ except ModelTypeError:
+ pass
+ assert model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ctd)
+
+ # get a dictionary of the ctd arguments where the values of the parameters
+ # given on the command line are overwritten
+ margs = model.parse_cl_args(cl_args=cliargs, ignore_required=True)
+
+ # write the ctd with the values taken from the dictionary
+ out = StringIO()
+ ctd_tree = model.write_ctd(out, margs)
+ print(out.getvalue())
diff -r 000000000000 -r 8fad84d1a74d generate-foo.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/generate-foo.sh Wed Sep 09 20:04:20 2020 +0000
@@ -0,0 +1,217 @@
+#!/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 $id"
+ echo ''
+
+ # get the tests from the CMakeLists.txt
+ # 1st remove some tests
+ # - Filefilter with empty select_palarity value (empty is not in the list of allowed options)
+ # - MassTraceExtractor with outdated ini file leading to wrong parameters https://github.com/OpenMS/OpenMS/issues/4386
+ # - OpenSwathMzMLFileCacher with -convert_back argumen https://github.com/OpenMS/OpenMS/issues/4399
+ # - IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differentlt
+ # - several tools with duplicated input (leads to conflict when linking)
+ # - TOFCalibration inputs we extension (also in prepare_test_data) https://github.com/OpenMS/OpenMS/pull/4525
+ # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456)
+ # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed)
+ # - some input files are originally in a subdir (degenerated cases/), but not in test-data
+ # - SeedListGenerator: https://github.com/OpenMS/OpenMS/issues/4404
+ # - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet)
+ CMAKE=$(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/${TMP_RIP_PATH}/""/' |
+ sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @' |
+ grep -v "MaRaClusterAdapter.*-consensus_out"|
+ grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " |
+ sed 's@degenerate_cases/@@g' |
+ grep -v 'TOPP_SeedListGenerator_3"' |
+ egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"')
+
+
+# grep -v 'FileFilter.*-spectra:select_polarity ""' |
+# grep -v 'MassTraceExtractor_2.ini ' |
+# grep -v "FileMerger_6_input2.mzML.*FileMerger_6_input2.mzML" |
+# grep -v "IDMerger_1_input1.idXML.*IDMerger_1_input1.idXML" |
+# grep -v "degenerated_empty.idXML.*degenerated_empty.idXML" |
+# grep -v "FeatureLinkerUnlabeledKD_1_output.consensusXML.*FeatureLinkerUnlabeledKD_1_output.consensusXML" |
+# grep -v "FeatureLinkerUnlabeledQT_1_output.consensusXML.*FeatureLinkerUnlabeledQT_1_output.consensusXML" |
+
+ # 1st part is a dirty hack to join lines containing a single function call, e.g.
+ # addtest(....
+ # ....)
+ echo "$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=" \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 ' /dev/null
+
+ #rm $testtmp
+ done
+ echo ''
+}
+
+#some tests use the same file twice which does not work in planemo tests
+#hence we create symlinks for each file used twice
+function unique_files {
+ line=$@
+ 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)?"
+ 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@${TMP_RIP_PATH}@dummy2.tmp@g'|
+ sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'|
+ while read line
+ do
+ test_id=$(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 $line)"
+ echo "$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 $test_id.stdout)\";fi"
+ done
+}
diff -r 000000000000 -r 8fad84d1a74d generate.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/generate.sh Wed Sep 09 20:04:20 2020 +0000
@@ -0,0 +1,76 @@
+#!/usr/bin/env bash
+
+# VERSION=2.3
+# CONDAPKG=https://anaconda.org/bioconda/openms/2.3.0/download/linux-64/openms-2.3.0-py27h932d754_3.tar.bz2
+# VERSION=2.4
+# CONDAPKG=https://anaconda.org/bioconda/openms/2.4.0/download/linux-64/openms-2.4.0-py27h574aadf_1.tar.bz2
+
+VERSION=2.5
+FILETYPES="filetypes.txt"
+PROFILE="20.05"
+## FILETYPES_RE=$(grep -v "^#" $FILETYPES | grep -v "^$" | cut -f 1 -d" " | tr '\n' '|' | sed 's/|$//'| sed 's/|/\\|/g')
+
+export tmp=$(mktemp -d)
+
+export CTDCONVERTER="$tmp/CTDConverter"
+
+export PYTHONPATH="$(pwd)/CTDopts/"
+###############################################################################
+## 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
+###############################################################################
+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$(cat convert.err)"; fi
+conda deactivate
+
+patch PepNovoAdapter.xml < PepNovoAdapter.patch
+patch OMSSAAdapter.xml < OMSSAAdapter.patch
+
+# #-b version log debug test in_type executable pepnovo_executable param_model_directory rt_concat_trafo_out param_id_pool
+
+# for i in A-E F-H I-L M-N O-P Q-Z
+# do
+# planemo t [$i]*xml --galaxy_branch release_20.05 --galaxy_python_version 3.7 --test_output $i.html --test_output_json $i.json &
+# done
diff -r 000000000000 -r 8fad84d1a74d hardcoded_params.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/hardcoded_params.json Wed Sep 09 20:04:20 2020 +0000
@@ -0,0 +1,247 @@
+{
+ "#": "blacklist parameters",
+
+ "version": [{"value": "@"}],
+ "debug": [{"value": "@"}],
+ "algorithm:debug": [{"value": "@"}],
+ "java_memory": [{"value": "@"}],
+ "java_permgen": [{"value": "@"}],
+ "#": "type of input is always determined from the file extension ",
+ "in_type": [{"value": "@"}],
+
+ "#": "tool specific blacklist parameters",
+
+ "convert_back": [{"value": "@", "tools": ["OpenSwathMzMLFileCacher"]}],
+ "NET_executable": [{
+ "value": "@",
+ "tools": ["FileConverter"]
+ }],
+
+
+ "params_file": [{"value": "@", "tools": ["SpectraSTSearchAdapter"]}],
+
+ "#": "TODO not usable in 2.5 https://github.com/OpenMS/OpenMS/issues/4456, corresponding test currently disabled",
+ "consensus_out": [{"value": "@", "tools": ["MaRaClusterAdapter"]}],
+ "#": "TODO would need treatment as prefix-output",
+ "output_directory": [{"value": "@", "tools": ["MaRaClusterAdapter"]}],
+
+ "#": "hardcode parameter values",
+
+ "comet_version": [{
+ "value":"2016.01 rev. 3"
+ }],
+ "comet_executable": [{
+ "value":"comet"
+ }],
+ "crux_executable": [{
+ "value": "crux"
+ }],
+ "fido_executable": [{
+ "value":"Fido"
+ }],
+ "fidocp_executable": [{
+ "value":"FidoChooseParameters"
+ }],
+ "maracluster_executable": [{
+ "value":"/home/berntm/projects/tools-galaxyp/tools/openms/OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster"
+ }],
+ "mascot_directory": [{
+ "value":"TODO"
+ }],
+ "myrimatch_executable": [{
+ "value":"myrimatch"
+ }],
+ "omssa_executable": [{
+ "value":"$(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}"
+ }],
+ "#": "hardcode the outer loop threads for OpenSwathWorkflow",
+ "outer_loop_threads": [{
+ "value": "1",
+ "tools": ["OpenSwathWorkflow"]
+ }],
+ "separator": [{
+ "value": ",",
+ "tools": ["IDMassAccuracy"]
+ }],
+ "#": "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",
+ "#": "MascotAdapter: https://github.com/OpenMS/OpenMS/pull/4553",
+ "#": "Phosphoscoring: https://github.com/OpenMS/OpenMS/pull/4569",
+ "#": "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:restrictions": "idXML",
+ "tools": ["MascotAdapter"]
+ }, {
+ "CTD:restrictions": "idXML",
+ "tools": ["PhosphoScoring"]
+ }, {
+ "CTD:type": "output-prefix",
+ "CTD:required": "true",
+ "CTD:restrictions": "mzml",
+ "tools": ["MzMLSplitter"]
+ }, {
+ "value": "@",
+ "tools": ["IDRipper"]
+ }],
+
+ "#": "https://github.com/OpenMS/OpenMS/pull/4552 .. if this is removed the test will need out_cm_FLAG",
+ "out_cm": [{
+ "CTD:required": true,
+ "tools": ["MetaboliteAdductDecharger"]
+ }],
+
+
+ "#": "https://github.com/OpenMS/OpenMS/pull/4451",
+ "out_xquestxml": [{
+ "CTD:restrictions": "xquest.xml",
+ "tools": ["OpenPepXL", "OpenPepXLLF"]
+ }],
+ "out_xquest_specxml": [{
+ "CTD:restrictions": "spec.xml",
+ "tools": ["OpenPepXL", "OpenPepXLLF"]
+ }],
+
+ "#": "Try to remove xml data type whereever possible",
+ "#": "XTandem Adapter output is called .xml in OMS -> 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",
+ "#": "SpectraSTSearchAdapter does not need xml .. redundant with pep.xml TODO check if list is up to date with each new release",
+ "#": "SeedListGenerator 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": "txt,tsv,pep.xml,pepXML,html",
+ "tools": ["SpectraSTSearchAdapter"]
+ }, {
+ "CTD:restrictions": "mzML,idXML,featureXML",
+ "tools": ["SeedListGenerator"]
+ }],
+
+ "#": "parameter is a flag but restrictions in wrong order: TODO https://github.com/OpenMS/OpenMS/pull/4455",
+ "# masstrace_snr_filtering": [{
+ "CTD:restrictions": "true,false",
+ "tools": ["MassTraceExtractor"]
+ }],
+
+ "#": "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"]
+ }],
+
+ "#": "output-prefix",
+ "out_path": [{
+ "CTD:type": "output-prefix",
+ "CTD:required": "true",
+ "CTD:restrictions": "idXML",
+ "tools": ["IDRipper"]
+ }],
+ "outputDirectory": [{
+ "CTD:type": "output-prefix",
+ "CTD:required": "true",
+ "CTD:restrictions": "mzml",
+ "tools": ["OpenSwathFileSplitter"]
+ }]
+}
diff -r 000000000000 -r 8fad84d1a74d macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Sep 09 20:04:20 2020 +0000
@@ -0,0 +1,129 @@
+
+
+
+ 2.5
+ 0
+
+
+ openms
+ openms-thirdparty
+
+ blast
+ openjdk
+
+
+
+ ctdopts
+
+
+
+
+
+
+
+
+
+
+
+
+ doi:10.1186/1471-2105-9-163
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ^[^$]
+
+ ^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ^ *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?( *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* *$
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$
+
+
+
+
+
+
+
+
+
+
+
+
+#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
+
+
+
diff -r 000000000000 -r 8fad84d1a74d macros_autotest.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros_autotest.xml Wed Sep 09 20:04:20 2020 +0000
@@ -0,0 +1,26318 @@
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diff -r 000000000000 -r 8fad84d1a74d macros_discarded_auto.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros_discarded_auto.xml Wed Sep 09 20:04:20 2020 +0000
@@ -0,0 +1,378 @@
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diff -r 000000000000 -r 8fad84d1a74d macros_test.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros_test.xml Wed Sep 09 20:04:20 2020 +0000
@@ -0,0 +1,549 @@
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diff -r 000000000000 -r 8fad84d1a74d prepare_test_data.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/prepare_test_data.sh Wed Sep 09 20:04:20 2020 +0000
@@ -0,0 +1,1196 @@
+export COMET_BINARY="comet"
+export CRUX_BINARY="crux"
+export FIDOCHOOSEPARAMS_BINARY="FidoChooseParameters"
+export FIDO_BINARY="Fido"
+export LUCIPHOR_BINARY="$(dirname $(realpath $(which luciphor2)))/luciphor2.jar"
+export MARACLUSTER_BINARY="/tmp/openms-stuff//OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster"
+export MSFRAGGER_BINARY="/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar"
+export MSGFPLUS_BINARY="$(msgf_plus -get_jar_path)"
+export MYRIMATCH_BINARY="myrimatch"
+export NOVOR_BINARY="/home/berntm/Downloads/novor/lib/novor.jar"
+export OMSSA_BINARY="$(dirname $(realpath $(which omssacl)))/omssacl"
+export PERCOLATOR_BINARY="percolator"
+export SIRIUS_BINARY="$(which sirius)"
+export SPECTRAST_BINARY="spectrast"
+export XTANDEM_BINARY="xtandem"
+export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"
+FuzzyDiff -test -ini FuzzyDiff.ini -in1 FuzzyDiff_3_in1.featureXML -in2 FuzzyDiff_3_in2.featureXML > UTILS_FuzzyDiff_3.stdout 2> UTILS_FuzzyDiff_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_FuzzyDiff_3 failed'; >&2 echo -e "stderr:\n$(cat UTILS_FuzzyDiff_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_FuzzyDiff_3.stdout)";fi
+IDMerger -test -in IDMerger_1_input1.idXML IDMerger_1_input2.idXML -out IDMerger_1_output.tmp -annotate_file_origin > TOPP_IDMerger_1.stdout 2> TOPP_IDMerger_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMerger_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMerger_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMerger_1.stdout)";fi
+IDMerger -test -pepxml_protxml -in IDMerger_2_input1.idXML IDMerger_2_input2.idXML -out IDMerger_2_output.tmp > TOPP_IDMerger_2.stdout 2> TOPP_IDMerger_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMerger_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMerger_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMerger_2.stdout)";fi
+IDMerger -test -in IDMerger_1_input1.idXML IDMerger_1_input1.idXML -out IDMerger_3_output.tmp > TOPP_IDMerger_3.stdout 2> TOPP_IDMerger_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMerger_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMerger_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMerger_3.stdout)";fi
+IDMerger -test -in degenerated_empty.idXML degenerated_empty.idXML -out IDMerger_4_output.tmp > TOPP_IDMerger_4.stdout 2> TOPP_IDMerger_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMerger_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMerger_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMerger_4.stdout)";fi
+IDMerger -test -in IDMerger_2_input1.idXML -add_to IDMerger_5_input1.idXML -out IDMerger_5_output.tmp > TOPP_IDMerger_5.stdout 2> TOPP_IDMerger_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMerger_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMerger_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMerger_5.stdout)";fi
+BaselineFilter -test -in BaselineFilter_input.mzML -out BaselineFilter.tmp -struc_elem_length 1.5 > TOPP_BaselineFilter_1.stdout 2> TOPP_BaselineFilter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_BaselineFilter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_BaselineFilter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_BaselineFilter_1.stdout)";fi
+ConsensusMapNormalizer -test -in ConsensusMapNormalizer_input.consensusXML -out ConsensusMapNormalizer.tmp > TOPP_ConsensusMapNormalizer_1.stdout 2> TOPP_ConsensusMapNormalizer_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConsensusMapNormalizer_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConsensusMapNormalizer_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConsensusMapNormalizer_1.stdout)";fi
+MapNormalizer -test -in MapNormalizer_input.mzML -out MapNormalizer.tmp > TOPP_MapNormalizer_1.stdout 2> TOPP_MapNormalizer_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapNormalizer_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapNormalizer_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapNormalizer_1.stdout)";fi
+Decharger -test -in Decharger_input.featureXML -ini Decharger_input.ini -out_fm Decharger_output_fm.tmp -out_cm Decharger_output.tmp -outpairs Decharger_p_output.tmp > TOPP_Decharger_1.stdout 2> TOPP_Decharger_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_Decharger_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_Decharger_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_Decharger_1.stdout)";fi
+DTAExtractor -test -in DTAExtractor_1_input.mzML -out DTAExtractor -rt :61 > TOPP_DTAExtractor_1.stdout 2> TOPP_DTAExtractor_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_DTAExtractor_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_DTAExtractor_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_DTAExtractor_1.stdout)";fi
+DTAExtractor -test -in DTAExtractor_1_input.mzML -out DTAExtractor -level 1 > TOPP_DTAExtractor_2.stdout 2> TOPP_DTAExtractor_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_DTAExtractor_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_DTAExtractor_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_DTAExtractor_2.stdout)";fi
+DTAExtractor -test -in DTAExtractor_1_input.mzML -out DTAExtractor -level 2 -mz :1000 > TOPP_DTAExtractor_3.stdout 2> TOPP_DTAExtractor_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_DTAExtractor_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_DTAExtractor_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_DTAExtractor_3.stdout)";fi
+MassTraceExtractor -test -ini MassTraceExtractor.ini -in MassTraceExtractor_1_input.mzML -out MassTraceExtractor_1.tmp > TOPP_MassTraceExtractor_1.stdout 2> TOPP_MassTraceExtractor_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MassTraceExtractor_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MassTraceExtractor_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MassTraceExtractor_1.stdout)";fi
+MassTraceExtractor -test -ini MassTraceExtractor_2.ini -in MassTraceExtractor_1_input.mzML -out MassTraceExtractor_2.tmp > TOPP_MassTraceExtractor_2.stdout 2> TOPP_MassTraceExtractor_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MassTraceExtractor_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MassTraceExtractor_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MassTraceExtractor_2.stdout)";fi
+FeatureFinderMetabo -test -ini FeatureFinderMetabo.ini -in FeatureFinderMetabo_1_input.mzML -out FeatureFinderMetabo_1.tmp > TOPP_FeatureFinderMetabo_1.stdout 2> TOPP_FeatureFinderMetabo_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMetabo_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMetabo_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMetabo_1.stdout)";fi
+FeatureFinderMetabo -test -ini FeatureFinderMetabo_2_noEPD.ini -in FeatureFinderMetabo_2_input.mzML -out FeatureFinderMetabo_2.tmp > TOPP_FeatureFinderMetabo_2.stdout 2> TOPP_FeatureFinderMetabo_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMetabo_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMetabo_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMetabo_2.stdout)";fi
+FeatureFinderMetabo -test -ini FeatureFinderMetabo_3.ini -in FeatureFinderMetabo_3_input.mzML -out FeatureFinderMetabo_3.tmp -out_chrom FeatureFinderMetabo_3_chrom.tmp > TOPP_FeatureFinderMetabo_3.stdout 2> TOPP_FeatureFinderMetabo_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMetabo_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMetabo_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMetabo_3.stdout)";fi
+FeatureFinderMetabo -test -ini FeatureFinderMetabo_4.ini -in FeatureFinderMetabo_3_input.mzML -out FeatureFinderMetabo_4.tmp -out_chrom FeatureFinderMetabo_4_chrom.tmp > TOPP_FeatureFinderMetabo_4.stdout 2> TOPP_FeatureFinderMetabo_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMetabo_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMetabo_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMetabo_4.stdout)";fi
+FeatureFinderMetabo -test -ini FeatureFinderMetabo.ini -in FeatureFinderMetabo_1_input.mzML -out FeatureFinderMetabo_5.tmp -algorithm:mtd:quant_method max_height > TOPP_FeatureFinderMetabo_5.stdout 2> TOPP_FeatureFinderMetabo_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMetabo_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMetabo_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMetabo_5.stdout)";fi
+FeatureFinderCentroided -test -ini FeatureFinderCentroided_1_parameters.ini -in FeatureFinderCentroided_1_input.mzML -out FeatureFinderCentroided_1.tmp > TOPP_FeatureFinderCentroided_1.stdout 2> TOPP_FeatureFinderCentroided_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderCentroided_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderCentroided_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderCentroided_1.stdout)";fi
+FeatureFinderIdentification -test -in FeatureFinderIdentification_1_input.mzML -id FeatureFinderIdentification_1_input.idXML -out FeatureFinderIdentification_1.tmp -extract:mz_window 0.1 -detect:peak_width 60 -model:type none > TOPP_FeatureFinderIdentification_1.stdout 2> TOPP_FeatureFinderIdentification_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderIdentification_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderIdentification_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderIdentification_1.stdout)";fi
+FeatureFinderIdentification -test -in FeatureFinderIdentification_1_input.mzML -id FeatureFinderIdentification_1_input.idXML -out FeatureFinderIdentification_3.tmp -extract:mz_window 0.1 -detect:peak_width 60 -model:type symmetric > TOPP_FeatureFinderIdentification_3.stdout 2> TOPP_FeatureFinderIdentification_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderIdentification_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderIdentification_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderIdentification_3.stdout)";fi
+FeatureFinderIdentification -test -in FeatureFinderIdentification_1_input.mzML -id FeatureFinderIdentification_1_input.idXML -out FeatureFinderIdentification_4.tmp -extract:mz_window 0.1 -extract:batch_size 10 -detect:peak_width 60 -model:type none > TOPP_FeatureFinderIdentification_4.stdout 2> TOPP_FeatureFinderIdentification_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderIdentification_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderIdentification_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderIdentification_4.stdout)";fi
+FeatureFinderMRM -test -in FeatureFinderMRM_1_input.mzML -ini FeatureFinderMRM_1_parameters.ini -out FeatureFinderMRM_1.tmp > TOPP_FeatureFinderMRM_1.stdout 2> TOPP_FeatureFinderMRM_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMRM_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMRM_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMRM_1.stdout)";fi
+FeatureFinderMultiplex -test -in FeatureFinderMultiplex_1_input.mzML -ini FeatureFinderMultiplex_1_parameters.ini -out FeatureFinderMultiplex_1.tmp -out_multiplets FeatureFinderMultiplex_2.tmp > TOPP_FeatureFinderMultiplex_1.stdout 2> TOPP_FeatureFinderMultiplex_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_1.stdout)";fi
+FeatureFinderMultiplex -test -in FeatureFinderMultiplex_2_input.mzML -ini FeatureFinderMultiplex_2_parameters.ini -out FeatureFinderMultiplex_3.tmp -out_multiplets FeatureFinderMultiplex_4.tmp > TOPP_FeatureFinderMultiplex_2.stdout 2> TOPP_FeatureFinderMultiplex_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_2.stdout)";fi
+FeatureFinderMultiplex -test -in FeatureFinderMultiplex_3_input.mzML -ini FeatureFinderMultiplex_3_parameters.ini -out FeatureFinderMultiplex_5.tmp -out_multiplets FeatureFinderMultiplex_6.tmp > TOPP_FeatureFinderMultiplex_3.stdout 2> TOPP_FeatureFinderMultiplex_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_3.stdout)";fi
+FeatureFinderMultiplex -test -in FeatureFinderMultiplex_4_input.mzML -ini FeatureFinderMultiplex_4_parameters.ini -out FeatureFinderMultiplex_7.tmp -out_multiplets FeatureFinderMultiplex_8.tmp > TOPP_FeatureFinderMultiplex_4.stdout 2> TOPP_FeatureFinderMultiplex_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_4.stdout)";fi
+FeatureFinderMultiplex -test -in FeatureFinderMultiplex_5_input.mzML -ini FeatureFinderMultiplex_5_parameters.ini -out FeatureFinderMultiplex_9.tmp -out_multiplets FeatureFinderMultiplex_10.tmp > TOPP_FeatureFinderMultiplex_5.stdout 2> TOPP_FeatureFinderMultiplex_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_5.stdout)";fi
+FeatureFinderMultiplex -test -in FeatureFinderMultiplex_6_input.mzML -ini FeatureFinderMultiplex_6_parameters.ini -out FeatureFinderMultiplex_11.tmp -out_multiplets FeatureFinderMultiplex_12.tmp > TOPP_FeatureFinderMultiplex_6.stdout 2> TOPP_FeatureFinderMultiplex_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_6.stdout)";fi
+FeatureFinderMultiplex -test -in FeatureFinderMultiplex_7_input.mzML -ini FeatureFinderMultiplex_7_parameters.ini -out FeatureFinderMultiplex_13.tmp -out_multiplets FeatureFinderMultiplex_14.tmp > TOPP_FeatureFinderMultiplex_7.stdout 2> TOPP_FeatureFinderMultiplex_7.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_7.stdout)";fi
+FeatureFinderMultiplex -test -in FeatureFinderMultiplex_8_input.mzML -ini FeatureFinderMultiplex_8_parameters.ini -out FeatureFinderMultiplex_15.tmp -out_multiplets FeatureFinderMultiplex_16.tmp > TOPP_FeatureFinderMultiplex_8.stdout 2> TOPP_FeatureFinderMultiplex_8.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_8.stdout)";fi
+FeatureFinderMultiplex -test -in FeatureFinderMultiplex_9_input.mzML -ini FeatureFinderMultiplex_9_parameters.ini -out FeatureFinderMultiplex_17.tmp -out_multiplets FeatureFinderMultiplex_18.tmp > TOPP_FeatureFinderMultiplex_9.stdout 2> TOPP_FeatureFinderMultiplex_9.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_9.stdout)";fi
+FeatureFinderMultiplex -test -in FeatureFinderMultiplex_10_input.mzML -ini FeatureFinderMultiplex_10_parameters.ini -out FeatureFinderMultiplex_19.tmp -out_multiplets FeatureFinderMultiplex_20.tmp > TOPP_FeatureFinderMultiplex_10.stdout 2> TOPP_FeatureFinderMultiplex_10.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_10.stdout)";fi
+FeatureFinderMultiplex -test -in FeatureFinderMultiplex_11_input.mzML -ini FeatureFinderMultiplex_11_parameters.ini -out FeatureFinderMultiplex_21.tmp > TOPP_FeatureFinderMultiplex_11.stdout 2> TOPP_FeatureFinderMultiplex_11.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureFinderMultiplex_11 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureFinderMultiplex_11.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureFinderMultiplex_11.stdout)";fi
+FileConverter -test -in FileConverter_1_input.mzData -out FileConverter_1.tmp -out_type mzML > TOPP_FileConverter_1.stdout 2> TOPP_FileConverter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_1.stdout)";fi
+FileConverter -test -in FileConverter_2_input.someInputDTA2D -in_type dta2d -out FileConverter_2.tmp -out_type mzML > TOPP_FileConverter_2.stdout 2> TOPP_FileConverter_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_2.stdout)";fi
+FileConverter -test -in FileConverter_3_input.featureXML -out FileConverter_3.tmp -out_type mzML > TOPP_FileConverter_3.stdout 2> TOPP_FileConverter_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_3.stdout)";fi
+FileConverter -test -in FileConverter_4_input.mzXML -out FileConverter_4.tmp -out_type mzML > TOPP_FileConverter_4.stdout 2> TOPP_FileConverter_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_4.stdout)";fi
+FileConverter -test -in FileConverter_5_input.mzML -out FileConverter_5.tmp -out_type mzXML > TOPP_FileConverter_5.stdout 2> TOPP_FileConverter_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_5.stdout)";fi
+FileConverter -test -in FileConverter_6_input.mzML -out FileConverter_6.tmp -out_type mzXML > TOPP_FileConverter_6.stdout 2> TOPP_FileConverter_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_6.stdout)";fi
+FileConverter -test -in FileConverter_7_input.consensusXML -out FileConverter_7.tmp -out_type featureXML > TOPP_FileConverter_7.stdout 2> TOPP_FileConverter_7.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_7.stdout)";fi
+FileConverter -test -in FileConverter_8_input.mzML -out FileConverter_8.tmp -out_type mzData > TOPP_FileConverter_8.stdout 2> TOPP_FileConverter_8.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_8.stdout)";fi
+FileConverter -test -in FileConverter_9_input.consensusXML -out FileConverter_9.tmp -out_type featureXML > TOPP_FileConverter_9.stdout 2> TOPP_FileConverter_9.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_9.stdout)";fi
+FileConverter -test -in FileConverter_10_input.edta -no_progress -out FileConverter_10.tmp -out_type featureXML > TOPP_FileConverter_10.stdout 2> TOPP_FileConverter_10.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_10.stdout)";fi
+FileConverter -test -in FileConverter_11_input.peplist -no_progress -out FileConverter_11.tmp -out_type featureXML > TOPP_FileConverter_11.stdout 2> TOPP_FileConverter_11.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_11 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_11.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_11.stdout)";fi
+FileConverter -test -in FileConverter_12_input.peptides.tsv -no_progress -out FileConverter_12.tmp -out_type featureXML > TOPP_FileConverter_12.stdout 2> TOPP_FileConverter_12.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_12 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_12.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_12.stdout)";fi
+FileConverter -test -in FileConverter_13_input.peptides.kroenik -no_progress -out FileConverter_13.tmp -out_type featureXML > TOPP_FileConverter_13.stdout 2> TOPP_FileConverter_13.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_13 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_13.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_13.stdout)";fi
+FileConverter -test -in FileConverter_9_output.featureXML -no_progress -out FileConverter_14.tmp -out_type consensusXML > TOPP_FileConverter_14.stdout 2> TOPP_FileConverter_14.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_14 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_14.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_14.stdout)";fi
+FileConverter -test -in FileConverter_10_input.edta -no_progress -out FileConverter_15.tmp -out_type consensusXML > TOPP_FileConverter_15.stdout 2> TOPP_FileConverter_15.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_15 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_15.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_15.stdout)";fi
+FileConverter -test -in FileConverter_16_input.edta -no_progress -out FileConverter_16.tmp -out_type consensusXML > TOPP_FileConverter_16.stdout 2> TOPP_FileConverter_16.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_16 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_16.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_16.stdout)";fi
+FileConverter -test -in FileConverter_17_input.consensusXML -no_progress -out FileConverter_17.csv > TOPP_FileConverter_17.stdout 2> TOPP_FileConverter_17.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_17 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_17.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_17.stdout)";fi
+FileConverter -test -in FileConverter_17_input.consensusXML -no_progress -out FileConverter_18.tmp -out_type csv > TOPP_FileConverter_18.stdout 2> TOPP_FileConverter_18.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_18 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_18.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_18.stdout)";fi
+FileConverter -test -in FileFilter_1_input.mzML -out FileConverter_19.tmp -process_lowmemory -in_type mzML -out_type mzML > TOPP_FileConverter_19.stdout 2> TOPP_FileConverter_19.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_19 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_19.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_19.stdout)";fi
+FileConverter -test -in FileConverter_20_input.featureXML -out FileConverter_20.tmp -in_type featureXML -out_type featureXML > TOPP_FileConverter_20.stdout 2> TOPP_FileConverter_20.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_20 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_20.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_20.stdout)";fi
+FileConverter -test -in FileConverter_4_input.mzXML -out FileConverter_21.tmp -out_type mzML -process_lowmemory > TOPP_FileConverter_21.stdout 2> TOPP_FileConverter_21.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_21 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_21.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_21.stdout)";fi
+FileConverter -test -in FileConverter_23_input.mzML -out FileConverter_23.tmp -out_type mzML > TOPP_FileConverter_23.stdout 2> TOPP_FileConverter_23.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_23 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_23.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_23.stdout)";fi
+FileConverter -test -in FileFilter_1_input.mzML -out FileConverter_24.tmp -process_lowmemory -in_type mzML -out_type mzML -lossy_compression -lossy_mass_accuracy 0.0001 > TOPP_FileConverter_24.stdout 2> TOPP_FileConverter_24.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_24 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_24.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_24.stdout)";fi
+FileConverter -test -in FileFilter_1_input.mzML -out FileConverter_25.tmp -process_lowmemory -in_type mzML -out_type mzML -lossy_compression > TOPP_FileConverter_25.stdout 2> TOPP_FileConverter_25.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_25 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_25.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_25.stdout)";fi
+FileConverter -test -in FileFilter_1_input.mzML -out FileConverter_26.tmp -force_MaxQuant_compatibility -out_type mzXML > TOPP_FileConverter_26.stdout 2> TOPP_FileConverter_26.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_26 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_26.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_26.stdout)";fi
+FileConverter -test -in FileConverter_26_output.mzXML -out FileConverter_26-2.tmp -force_MaxQuant_compatibility -out_type mzXML > TOPP_FileConverter_26-2.stdout 2> TOPP_FileConverter_26-2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_26-2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_26-2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_26-2.stdout)";fi
+FileConverter -test -in FileConverter_27_input.mzML -out FileConverter_27.tmp -out_type mzML -convert_to_chromatograms > TOPP_FileConverter_27.stdout 2> TOPP_FileConverter_27.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_27 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_27.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_27.stdout)";fi
+FileConverter -test -in FileConverter_28_input.mzML -out FileConverter_28.tmp -out_type mzML -convert_to_chromatograms > TOPP_FileConverter_28.stdout 2> TOPP_FileConverter_28.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_28 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_28.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_28.stdout)";fi
+FileConverter -test -in OpenSwathWorkflow_17_input.mzML -out FileConverter_29.tmp -out_type mzML -lossy_compression -lossy_mass_accuracy 1e-5 -process_lowmemory > TOPP_FileConverter_29.stdout 2> TOPP_FileConverter_29.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_29 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_29.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_29.stdout)";fi
+FileConverter -test -in FileConverter_29.tmp -in_type mzML -out FileConverter_29.back.tmp -out_type mzML > TOPP_FileConverter_29_back.stdout 2> TOPP_FileConverter_29_back.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_29_back failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_29_back.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_29_back.stdout)";fi
+FileConverter -test -in FileConverter_30_input.mzML -change_im_format multiple -out_type mzML -out FileConverter_30.tmp > TOPP_FileConverter_30.stdout 2> TOPP_FileConverter_30.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_30 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_30.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_30.stdout)";fi
+FileConverter -test -in FileConverter_30_output.mzML -change_im_format single -out_type mzML -out FileConverter_31.tmp > TOPP_FileConverter_31.stdout 2> TOPP_FileConverter_31.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileConverter_31 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileConverter_31.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileConverter_31.stdout)";fi
+FileFilter -test -in FileFilter_1_input.mzML -out FileFilter_1.tmp -rt :30 -mz :1000 -int :20000 -in_type mzML -out_type mzML > TOPP_FileFilter_1.stdout 2> TOPP_FileFilter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_1.stdout)";fi
+FileFilter -test -in FileFilter_1_input.mzML -out FileFilter_2.tmp -rt 30: -mz 1000: -int 100: -in_type mzML -out_type mzML > TOPP_FileFilter_2.stdout 2> TOPP_FileFilter_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_2.stdout)";fi
+FileFilter -test -in FileFilter_1_input.mzML -out FileFilter_3.tmp -peak_options:level 2 -in_type mzML -out_type mzML > TOPP_FileFilter_3.stdout 2> TOPP_FileFilter_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_3.stdout)";fi
+FileFilter -test -in FileFilter_4_input.mzML -out FileFilter_4.tmp -spectra:remove_zoom -in_type mzML -out_type mzML > TOPP_FileFilter_4.stdout 2> TOPP_FileFilter_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_4.stdout)";fi
+FileFilter -test -in FileFilter_5_input.featureXML -out FileFilter_5.tmp -rt :1000 -mz :480 -int :79000 -f_and_c:charge :3 -feature:q :0.6 -in_type featureXML -out_type featureXML > TOPP_FileFilter_5.stdout 2> TOPP_FileFilter_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_5.stdout)";fi
+FileFilter -test -in FileFilter_5_input.featureXML -out FileFilter_6.tmp -rt 1000: -mz 440: -int 70000: -f_and_c:charge 3: -feature:q 0.51: -in_type featureXML -out_type featureXML > TOPP_FileFilter_6.stdout 2> TOPP_FileFilter_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_6.stdout)";fi
+FileFilter -test -in FileFilter_7_input.mzML -out FileFilter_7.tmp -int 7000: -peak_options:level 1 2 3 -in_type mzML -out_type mzML > TOPP_FileFilter_7.stdout 2> TOPP_FileFilter_7.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_7.stdout)";fi
+FileFilter -test -in FileFilter_8_input.consensusXML -out FileFilter_8.tmp -rt 600:1400 -mz 700:2300 -int 1100:6000 -in_type consensusXML -out_type consensusXML > TOPP_FileFilter_8.stdout 2> TOPP_FileFilter_8.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_8.stdout)";fi
+FileFilter -test -in FileFilter_9_input.mzML -out FileFilter_9.tmp -spectra:remove_mode SelectedIonMonitoring -in_type mzML -out_type mzML > TOPP_FileFilter_9.stdout 2> TOPP_FileFilter_9.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_9.stdout)";fi
+FileFilter -test -in FileFilter_10_input.mzML -out FileFilter_10.tmp -spectra:remove_activation "Collision-induced dissociation" -in_type mzML -out_type mzML > TOPP_FileFilter_10.stdout 2> TOPP_FileFilter_10.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_10.stdout)";fi
+FileFilter -test -in FileFilter_11_input.mzML -out FileFilter_11.tmp -spectra:remove_activation "Plasma desorption" -in_type mzML -out_type mzML > TOPP_FileFilter_11.stdout 2> TOPP_FileFilter_11.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_11 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_11.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_11.stdout)";fi
+FileFilter -test -in FileFilter_12_input.mzML -out FileFilter_12.tmp -peak_options:remove_chromatograms -in_type mzML -out_type mzML > TOPP_FileFilter_12.stdout 2> TOPP_FileFilter_12.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_12 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_12.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_12.stdout)";fi
+FileFilter -test -in FileFilter_13_input.consensusXML -out FileFilter_13.tmp -in_type consensusXML -out_type featureXML -consensus:map 2 > TOPP_FileFilter_13.stdout 2> TOPP_FileFilter_13.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_13 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_13.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_13.stdout)";fi
+FileFilter -test -in FileFilter_14_input.consensusXML -out FileFilter_14.tmp -in_type consensusXML -out_type consensusXML -consensus:map 0 2 > TOPP_FileFilter_14.stdout 2> TOPP_FileFilter_14.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_14 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_14.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_14.stdout)";fi
+FileFilter -test -in FileFilter_15_input.featureXML -out FileFilter_15.tmp -id:sequences_whitelist Oxidation -id:remove_unassigned_ids > TOPP_FileFilter_15.stdout 2> TOPP_FileFilter_15.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_15 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_15.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_15.stdout)";fi
+FileFilter -test -in FileFilter_15_input.featureXML -out FileFilter_16.tmp -id:sequences_whitelist Oxidation -id:remove_unassigned_ids -mz 400:600 -rt 3000:4000 > TOPP_FileFilter_16.stdout 2> TOPP_FileFilter_16.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_16 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_16.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_16.stdout)";fi
+FileFilter -test -in FileFilter_15_input.featureXML -out FileFilter_17.tmp -id:remove_annotated_features -mz 400:600 -rt 3000:4000 > TOPP_FileFilter_17.stdout 2> TOPP_FileFilter_17.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_17 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_17.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_17.stdout)";fi
+FileFilter -test -in FileFilter_18_input.consensusXML -out FileFilter_18.tmp -id:sequences_whitelist Oxidation -id:remove_unassigned_ids > TOPP_FileFilter_18.stdout 2> TOPP_FileFilter_18.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_18 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_18.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_18.stdout)";fi
+FileFilter -test -in FileFilter_18_input.consensusXML -out FileFilter_19.tmp -id:remove_unannotated_features -mz 400:600 -rt 3000:4000 > TOPP_FileFilter_19.stdout 2> TOPP_FileFilter_19.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_19 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_19.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_19.stdout)";fi
+FileFilter -test -in FileFilter_15_input.featureXML -out FileFilter_20.tmp -id:accessions_whitelist YDL217C -id:remove_unassigned_ids > TOPP_FileFilter_20.stdout 2> TOPP_FileFilter_20.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_20 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_20.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_20.stdout)";fi
+FileFilter -test -in FileFilter_15_input.featureXML -out FileFilter_21.tmp -id:remove_unassigned_ids -id:remove_unannotated_features -id:keep_best_score_id > TOPP_FileFilter_21.stdout 2> TOPP_FileFilter_21.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_21 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_21.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_21.stdout)";fi
+FileFilter -test -in FileFilter_22_input.consensusXML -out FileFilter_22.tmp -f_and_c:remove_meta distinct_charges gt "1,2" > TOPP_FileFilter_22.stdout 2> TOPP_FileFilter_22.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_22 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_22.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_22.stdout)";fi
+FileFilter -test -in FileFilter_22_input.consensusXML -out FileFilter_23.tmp -f_and_c:remove_meta distinct_charges_size gt 2 > TOPP_FileFilter_23.stdout 2> TOPP_FileFilter_23.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_23 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_23.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_23.stdout)";fi
+FileFilter -test -in FileFilter_22_input.consensusXML -out FileFilter_24.tmp -f_and_c:remove_meta DOESNOTEXIST lt "whatever" > TOPP_FileFilter_24.stdout 2> TOPP_FileFilter_24.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_24 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_24.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_24.stdout)";fi
+FileFilter -test -in FileFilter_25_input.mzML.gz -id:blacklist FileFilter_25_input.idXML -out FileFilter_25.tmp -id:mz 0.05 -id:rt 1 -id:blacklist_imperfect > TOPP_FileFilter_25.stdout 2> TOPP_FileFilter_25.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_25 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_25.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_25.stdout)";fi
+FileFilter -test -in FileFilter_25_input.mzML.gz -id:blacklist FileFilter_25_input.idXML -out FileFilter_26.tmp -id:blacklist_imperfect > TOPP_FileFilter_26.stdout 2> TOPP_FileFilter_26.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_26 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_26.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_26.stdout)";fi
+FileFilter -test -in FileFilter_28_input.mzML.gz -peak_options:pc_mz_range 832:836 -out FileFilter_28.tmp -peak_options:level 2 > TOPP_FileFilter_28.stdout 2> TOPP_FileFilter_28.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_28 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_28.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_28.stdout)";fi
+FileFilter -test -in FileFilter_28_input.mzML.gz -peak_options:pc_mz_range 832:836 -out FileFilter_29.tmp -peak_options:level 1 2 > TOPP_FileFilter_29.stdout 2> TOPP_FileFilter_29.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_29 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_29.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_29.stdout)";fi
+FileFilter -test -in FileFilter_28_input.mzML.gz -peak_options:pc_mz_range 832:836 -out FileFilter_30.tmp -peak_options:level 1 2 > TOPP_FileFilter_30.stdout 2> TOPP_FileFilter_30.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_30 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_30.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_30.stdout)";fi
+FileFilter -test -in FileFilter_31_34_input.mzML -spectra:remove_isolation_window_width :2 -out FileFilter_31.tmp > TOPP_FileFilter_31.stdout 2> TOPP_FileFilter_31.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_31 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_31.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_31.stdout)";fi
+FileFilter -test -in FileFilter_31_34_input.mzML -spectra:select_isolation_window_width :2 -out FileFilter_32.tmp > TOPP_FileFilter_32.stdout 2> TOPP_FileFilter_32.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_32 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_32.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_32.stdout)";fi
+FileFilter -test -in FileFilter_31_34_input.mzML -spectra:remove_collision_energy :35 -out FileFilter_33.tmp > TOPP_FileFilter_33.stdout 2> TOPP_FileFilter_33.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_33 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_33.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_33.stdout)";fi
+FileFilter -test -in FileFilter_31_34_input.mzML -spectra:select_collision_energy :35 -out FileFilter_34.tmp > TOPP_FileFilter_34.stdout 2> TOPP_FileFilter_34.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_34 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_34.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_34.stdout)";fi
+FileFilter -test -in FileFilter_1_input.mzML -out FileFilter_35.tmp -peak_options:indexed_file true -in_type mzML -out_type mzML > TOPP_FileFilter_35.stdout 2> TOPP_FileFilter_35.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_35 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_35.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_35.stdout)";fi
+FileFilter -test -in FileFilter_1_input.mzML -out FileFilter_36.tmp -peak_options:indexed_file false -in_type mzML -out_type mzML > TOPP_FileFilter_36.stdout 2> TOPP_FileFilter_36.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_36 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_36.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_36.stdout)";fi
+FileFilter -test -in FileFilter_1_input.mzML -out FileFilter_37.tmp -test -peak_options:numpress:intensity slof -peak_options:numpress:masstime linear -in_type mzML -peak_options:numpress:lossy_mass_accuracy 1e-4 -out_type mzML > TOPP_FileFilter_37.stdout 2> TOPP_FileFilter_37.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_37 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_37.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_37.stdout)";fi
+FileFilter -test -in FileFilter_1_input.mzML -out FileFilter_38.tmp -test -peak_options:numpress:intensity pic -peak_options:numpress:masstime linear -in_type mzML -peak_options:numpress:lossy_mass_accuracy 1e-4 -out_type mzML > TOPP_FileFilter_38.stdout 2> TOPP_FileFilter_38.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_38 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_38.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_38.stdout)";fi
+FileFilter -test -in FileFilter_40_input.mzML -out FileFilter_40.tmp -spectra:select_polarity positive -in_type mzML -out_type mzML > TOPP_FileFilter_40.stdout 2> TOPP_FileFilter_40.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_40 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_40.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_40.stdout)";fi
+FileFilter -test -in FileFilter_40_input.mzML -out FileFilter_41.tmp -spectra:select_polarity negative -in_type mzML -out_type mzML > TOPP_FileFilter_41.stdout 2> TOPP_FileFilter_41.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_41 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_41.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_41.stdout)";fi
+FileFilter -test -in FileFilter_40_input.mzML -out FileFilter_42.tmp -spectra:select_polarity "" -in_type mzML -out_type mzML > TOPP_FileFilter_42.stdout 2> TOPP_FileFilter_42.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_42 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_42.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_42.stdout)";fi
+FileFilter -test -in FileFilter_43_input.mzML -out FileFilter_43.tmp.mzML -in_type mzML -out_type mzML > TOPP_FileFilter_43.stdout 2> TOPP_FileFilter_43.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_43 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_43.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_43.stdout)";fi
+FileFilter -test -in FileFilter_43.tmp.mzML -out FileFilter_43.dummy.tmp -in_type mzML -out_type mzML > TOPP_FileFilter_43_read_again.stdout 2> TOPP_FileFilter_43_read_again.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_43_read_again failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_43_read_again.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_43_read_again.stdout)";fi
+FileFilter -test -in FileFilter_44_input.mzML -out FileFilter_44.tmp -test -in_type mzML -out_type mzML > TOPP_FileFilter_44.stdout 2> TOPP_FileFilter_44.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_44 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_44.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_44.stdout)";fi
+FileFilter -test -in FileFilter_45_input.featureXML -id:sequences_whitelist "YSFS" "STLIPPPSK(Label:13C(6)15N(2))" -out FileFilter_45.tmp > TOPP_FileFilter_45.stdout 2> TOPP_FileFilter_45.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_45 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_45.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_45.stdout)";fi
+FileFilter -test -in FileFilter_46_input.featureXML -id:sequences_whitelist "YSFS" "STLIPPPSK(Label:13C(6)15N(2))" -id:sequence_comparison_method "exact" -out FileFilter_46.tmp > TOPP_FileFilter_46.stdout 2> TOPP_FileFilter_46.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_46 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_46.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_46.stdout)";fi
+FileFilter -test -in FileFilter_47_input.mzML -spectra:blackorwhitelist:file FileFilter_47_input_select.mzML -spectra:blackorwhitelist:similarity_threshold 0.9 -out FileFilter_47_1.tmp > TOPP_FileFilter_47.stdout 2> TOPP_FileFilter_47.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_47 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_47.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_47.stdout)";fi
+FileFilter -test -in FileFilter_47_input.mzML -spectra:blackorwhitelist:file FileFilter_47_input_select.mzML -spectra:blackorwhitelist:similarity_threshold 0.9 -spectra:blackorwhitelist:blacklist false -out FileFilter_48_1.tmp > TOPP_FileFilter_48.stdout 2> TOPP_FileFilter_48.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_48 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_48.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_48.stdout)";fi
+FileFilter -test -in FileFilter_49_input.mzML -peak_options:numpress:intensity pic -peak_options:numpress:masstime linear -peak_options:numpress:float_da slof -peak_options:zlib_compression true -out FileFilter_49_1.tmp > TOPP_FileFilter_49.stdout 2> TOPP_FileFilter_49.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileFilter_49 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileFilter_49.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileFilter_49.stdout)";fi
+FileInfo -test -in FileInfo_1_input.dta -in_type dta -no_progress -out FileInfo_1.tmp > TOPP_FileInfo_1.stdout 2> TOPP_FileInfo_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_1.stdout)";fi
+FileInfo -test -in FileInfo_2_input.dta2d -no_progress -out FileInfo_2.tmp > TOPP_FileInfo_2.stdout 2> TOPP_FileInfo_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_2.stdout)";fi
+FileInfo -test -in FileInfo_3_input.featureXML -m -s -p -no_progress -out FileInfo_3.tmp > TOPP_FileInfo_3.stdout 2> TOPP_FileInfo_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_3.stdout)";fi
+FileInfo -test -in FileInfo_4_input.mzXML -m -no_progress -out FileInfo_4.tmp > TOPP_FileInfo_4.stdout 2> TOPP_FileInfo_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_4.stdout)";fi
+FileInfo -test -in FileInfo_5_input.mzDat -in_type mzData -m -s -no_progress -out FileInfo_5.tmp > TOPP_FileInfo_5.stdout 2> TOPP_FileInfo_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_5.stdout)";fi
+FileInfo -test -in FileInfo_6_input.mzData -d -s -no_progress -out FileInfo_6.tmp > TOPP_FileInfo_6.stdout 2> TOPP_FileInfo_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_6.stdout)";fi
+FileInfo -test -in FileInfo_7_input.consensusXML -s -m -p -no_progress -out FileInfo_7.tmp > TOPP_FileInfo_7.stdout 2> TOPP_FileInfo_7.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_7.stdout)";fi
+FileInfo -test -in FileInfo_9_input.mzML -m -p -s -no_progress -out FileInfo_9.tmp > TOPP_FileInfo_9.stdout 2> TOPP_FileInfo_9.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_9.stdout)";fi
+FileInfo -test -in FileInfo_10_input.idXML -no_progress -out FileInfo_10.tmp > TOPP_FileInfo_10.stdout 2> TOPP_FileInfo_10.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_10.stdout)";fi
+FileInfo -test -in FileInfo_12_input.mzML -i -no_progress > TOPP_FileInfo_12.stdout 2> TOPP_FileInfo_12.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_12 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_12.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_12.stdout)";fi
+FileInfo -test -in FileInfo_13_input.consensusXML -no_progress > TOPP_FileInfo_13.stdout 2> TOPP_FileInfo_13.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_13 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_13.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_13.stdout)";fi
+FileInfo -test -in FileInfo_14_input.mzid -v -no_progress -out FileInfo_14.tmp > TOPP_FileInfo_14.stdout 2> TOPP_FileInfo_14.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_14 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_14.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_14.stdout)";fi
+FileInfo -test -in FileInfo_15_input.mzid -v -no_progress -out FileInfo_15.tmp > TOPP_FileInfo_15.stdout 2> TOPP_FileInfo_15.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_15 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_15.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_15.stdout)";fi
+FileInfo -test -in FileInfo_16_input.trafoXML -out FileInfo_16_output.tmp > TOPP_FileInfo_16.stdout 2> TOPP_FileInfo_16.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_16 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_16.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_16.stdout)";fi
+FileInfo -test -in FileInfo_17_input.fasta -out FileInfo_17_output.tmp > TOPP_FileInfo_17.stdout 2> TOPP_FileInfo_17.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_17 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_17.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_17.stdout)";fi
+FileInfo -test -in FileInfo_18_input.fasta -out FileInfo_18_output.tmp > TOPP_FileInfo_18.stdout 2> TOPP_FileInfo_18.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileInfo_18 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileInfo_18.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileInfo_18.stdout)";fi
+FileMerger -test -in FileMerger_1_input1.dta2d FileMerger_1_input2.dta FileMerger_1_input3.dta2d -out FileMerger_1.tmp -raw:rt_custom 1 2 3 > TOPP_FileMerger_1.stdout 2> TOPP_FileMerger_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_1.stdout)";fi
+FileMerger -test -in FileMerger_2_input1.dta FileMerger_2_input2.dta -in_type dta -out FileMerger_2.tmp -raw:rt_custom 5 10 > TOPP_FileMerger_2.stdout 2> TOPP_FileMerger_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_2.stdout)";fi
+FileMerger -test -in FileMerger_3_input1.dta FileMerger_3_input2.dta -out FileMerger_3.tmp -raw:rt_auto > TOPP_FileMerger_3.stdout 2> TOPP_FileMerger_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_3.stdout)";fi
+FileMerger -test -in FileMerger_4_input1.dta2d FileMerger_4_input2.dta2d -out FileMerger_4.tmp > TOPP_FileMerger_4.stdout 2> TOPP_FileMerger_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_4.stdout)";fi
+FileMerger -test -in FileMerger_5_input_rt1023.331.dta FileMerger_5_input_rt2044.334.dta FileMerger_5_input_rt889.32.dta -raw:rt_filename -raw:ms_level 2 -out FileMerger_5.tmp > TOPP_FileMerger_5.stdout 2> TOPP_FileMerger_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_5.stdout)";fi
+FileMerger -test -in FileMerger_6_input1.mzML FileMerger_6_input2.mzML -out FileMerger_6.tmp > TOPP_FileMerger_6.stdout 2> TOPP_FileMerger_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_6.stdout)";fi
+FileMerger -test -in FileMerger_7_input1.featureXML FileMerger_7_input2.featureXML -out FileMerger_7.tmp > TOPP_FileMerger_7.stdout 2> TOPP_FileMerger_7.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_7.stdout)";fi
+FileMerger -test -in FileMerger_8_input1.consensusXML FileMerger_8_input2.consensusXML -out FileMerger_8.tmp > TOPP_FileMerger_8.stdout 2> TOPP_FileMerger_8.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_8.stdout)";fi
+FileMerger -test -in FileMerger_9_input1.traML FileMerger_9_input2.traML -out FileMerger_9.tmp > TOPP_FileMerger_9.stdout 2> TOPP_FileMerger_9.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_9.stdout)";fi
+FileMerger -test -in FileMerger_6_input2.mzML FileMerger_6_input2.mzML -out FileMerger_10_output.tmp -rt_concat:gap 10.0 -rt_concat:trafo_out FileMerger_10_trafo1.tmp FileMerger_10_trafo2.tmp > TOPP_FileMerger_10.stdout 2> TOPP_FileMerger_10.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_10.stdout)";fi
+FileMerger -test -in FileMerger_8_input1.consensusXML FileMerger_8_input2.consensusXML -append_method append_cols -out FileMerger_11.tmp > TOPP_FileMerger_11.stdout 2> TOPP_FileMerger_11.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FileMerger_11 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FileMerger_11.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FileMerger_11.stdout)";fi
+GNPSExport -test -in_cm GNPSExport_single.consensusXML -in_mzml GNPSExport_mz1.mzML -out GNPSExport_1_out.tmp -output_type full_spectra > TOPP_GNPSExport_1.stdout 2> TOPP_GNPSExport_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_GNPSExport_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_GNPSExport_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_GNPSExport_1.stdout)";fi
+GNPSExport -test -in_cm GNPSExport_single.consensusXML -in_mzml GNPSExport_mz1.mzML -out GNPSExport_2_out.tmp -output_type merged_spectra > TOPP_GNPSExport_2.stdout 2> TOPP_GNPSExport_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_GNPSExport_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_GNPSExport_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_GNPSExport_2.stdout)";fi
+GNPSExport -test -in_cm GNPSExport_merged.consensusXML -in_mzml GNPSExport_mz1.mzML GNPSExport_mz2.mzML -out GNPSExport_3_out.tmp -output_type full_spectra > TOPP_GNPSExport_3.stdout 2> TOPP_GNPSExport_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_GNPSExport_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_GNPSExport_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_GNPSExport_3.stdout)";fi
+GNPSExport -test -in_cm GNPSExport_merged.consensusXML -in_mzml GNPSExport_mz1.mzML GNPSExport_mz2.mzML -out GNPSExport_4_out.tmp > TOPP_GNPSExport_4.stdout 2> TOPP_GNPSExport_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_GNPSExport_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_GNPSExport_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_GNPSExport_4.stdout)";fi
+HighResPrecursorMassCorrector -test -in HighResPrecursorMassCorrector_2860_1103_3.mzML -feature:in HighResPrecursorMassCorrector_2860_1103_3.featureXML -out HighResPrecursorMassCorrector_2860_1103_3_out.tmp > TOPP_HighResPrecursorMassCorrector_1.stdout 2> TOPP_HighResPrecursorMassCorrector_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_HighResPrecursorMassCorrector_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_HighResPrecursorMassCorrector_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_HighResPrecursorMassCorrector_1.stdout)";fi
+HighResPrecursorMassCorrector -test -in HighResPrecursorMassCorrector_1035_1178_4.mzML -feature:in HighResPrecursorMassCorrector_1035_1178_4.featureXML -feature:max_trace 4 -feature:mz_tolerance 10 -out HighResPrecursorMassCorrector_1035_1178_4_out.tmp > TOPP_HighResPrecursorMassCorrector_2.stdout 2> TOPP_HighResPrecursorMassCorrector_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_HighResPrecursorMassCorrector_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_HighResPrecursorMassCorrector_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_HighResPrecursorMassCorrector_2.stdout)";fi
+HighResPrecursorMassCorrector -test -in HighResPrecursorMassCorrector_2538_1091_2.mzML -feature:in HighResPrecursorMassCorrector_2538_1091_2.featureXML -out HighResPrecursorMassCorrector_2538_1091_2_out.tmp > TOPP_HighResPrecursorMassCorrector_3.stdout 2> TOPP_HighResPrecursorMassCorrector_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_HighResPrecursorMassCorrector_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_HighResPrecursorMassCorrector_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_HighResPrecursorMassCorrector_3.stdout)";fi
+HighResPrecursorMassCorrector -test -in HighResPrecursorMassCorrector_2810_1091_3.mzML -feature:in HighResPrecursorMassCorrector_2810_1091_3.featureXML -out HighResPrecursorMassCorrector_2810_1091_3_out.tmp > TOPP_HighResPrecursorMassCorrector_4.stdout 2> TOPP_HighResPrecursorMassCorrector_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_HighResPrecursorMassCorrector_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_HighResPrecursorMassCorrector_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_HighResPrecursorMassCorrector_4.stdout)";fi
+HighResPrecursorMassCorrector -test -in HighResPrecursorMassCorrector_3070_1191_3.mzML -feature:in HighResPrecursorMassCorrector_3070_1191_3.featureXML -out HighResPrecursorMassCorrector_3070_1191_3_out.tmp > TOPP_HighResPrecursorMassCorrector_5.stdout 2> TOPP_HighResPrecursorMassCorrector_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_HighResPrecursorMassCorrector_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_HighResPrecursorMassCorrector_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_HighResPrecursorMassCorrector_5.stdout)";fi
+HighResPrecursorMassCorrector -test -in HighResPrecursorMassCorrector_6.mzML -highest_intensity_peak:mz_tolerance 0.2 -out HighResPrecursorMassCorrector_6_out.tmp > TOPP_HighResPrecursorMassCorrector_6.stdout 2> TOPP_HighResPrecursorMassCorrector_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_HighResPrecursorMassCorrector_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_HighResPrecursorMassCorrector_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_HighResPrecursorMassCorrector_6.stdout)";fi
+IDRTCalibration -test -in IDRTCalibration_1_input.idXML -out IDRTCalibration_1_output.tmp -calibrant_1_input 10 -calibrant_2_input 90 > TOPP_IDRTCalibration_1.stdout 2> TOPP_IDRTCalibration_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDRTCalibration_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDRTCalibration_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDRTCalibration_1.stdout)";fi
+IDRTCalibration -test -in degenerated_empty.idXML -out IDRTCalibration_2_output.tmp -calibrant_1_input 10 -calibrant_2_input 90 > TOPP_IDRTCalibration_2.stdout 2> TOPP_IDRTCalibration_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDRTCalibration_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDRTCalibration_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDRTCalibration_2.stdout)";fi
+IDMassAccuracy -test -in spectra.mzML -id_in MSGFPlusAdapter_1_out.idXML -number_of_bins 10 -out_fragment IDMassAccuracy_1_out_fragment.tsv -out_fragment_fit IDMassAccuracy_1_out_fragment_fit.tsv -out_precursor IDMassAccuracy_1_out_precursor.tsv -out_precursor_fit IDMassAccuracy_1_out_precursor_fit.tsv > TOPP_IDMassAccuracy_1.stdout 2> TOPP_IDMassAccuracy_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMassAccuracy_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMassAccuracy_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMassAccuracy_1.stdout)";fi
+IsobaricAnalyzer -test -in IsobaricAnalyzer_input_1.mzML -ini IsobaricAnalyzer.ini -out IsobaricAnalyzer_output_1.tmp > TOPP_IsobaricAnalyzer_1.stdout 2> TOPP_IsobaricAnalyzer_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IsobaricAnalyzer_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IsobaricAnalyzer_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IsobaricAnalyzer_1.stdout)";fi
+IsobaricAnalyzer -test -in TMTTenPlexMethod_test.mzML -ini TMTTenPlexMethod_test.ini -out TMTTenPlexMethod_output.tmp > TOPP_IsobaricAnalyzer_TMTTenPlexMethod_1.stdout 2> TOPP_IsobaricAnalyzer_TMTTenPlexMethod_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IsobaricAnalyzer_TMTTenPlexMethod_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IsobaricAnalyzer_TMTTenPlexMethod_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IsobaricAnalyzer_TMTTenPlexMethod_1.stdout)";fi
+IsobaricAnalyzer -test -in TMTTenPlexMethod_test.mzML -ini TMTElevenPlexMethod_test.ini -out TMTElevenPlexMethod_output.tmp > TOPP_IsobaricAnalyzer_TMTElevenPlexMethod_1.stdout 2> TOPP_IsobaricAnalyzer_TMTElevenPlexMethod_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IsobaricAnalyzer_TMTElevenPlexMethod_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IsobaricAnalyzer_TMTElevenPlexMethod_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IsobaricAnalyzer_TMTElevenPlexMethod_1.stdout)";fi
+IsobaricAnalyzer -test -in MS3_nonHierarchical.mzML -extraction:select_activation "Collision-induced dissociation" -type tmt10plex -out MS3TMT10Plex_output.tmp > TOPP_IsobaricAnalyzer_MS3TMT10Plex_1.stdout 2> TOPP_IsobaricAnalyzer_MS3TMT10Plex_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IsobaricAnalyzer_MS3TMT10Plex_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IsobaricAnalyzer_MS3TMT10Plex_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IsobaricAnalyzer_MS3TMT10Plex_1.stdout)";fi
+IDConflictResolver -test -in IDConflictResolver_1_input.featureXML -out IDConflictResolver_1_output.tmp > TOPP_IDConflictResolver_1.stdout 2> TOPP_IDConflictResolver_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDConflictResolver_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDConflictResolver_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDConflictResolver_1.stdout)";fi
+IDConflictResolver -test -in IDConflictResolver_2_input.consensusXML -out IDConflictResolver_2_output.tmp > TOPP_IDConflictResolver_2.stdout 2> TOPP_IDConflictResolver_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDConflictResolver_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDConflictResolver_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDConflictResolver_2.stdout)";fi
+IDConflictResolver -test -in IDConflictResolver_3_input.consensusXML -out IDConflictResolver_3_output.tmp > TOPP_IDConflictResolver_3.stdout 2> TOPP_IDConflictResolver_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDConflictResolver_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDConflictResolver_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDConflictResolver_3.stdout)";fi
+IDConflictResolver -test -in IDConflictResolver_4_input.featureXML -resolve_between_features highest_intensity -out IDConflictResolver_4.tmp > TOPP_IDConflictResolver_4.stdout 2> TOPP_IDConflictResolver_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDConflictResolver_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDConflictResolver_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDConflictResolver_4.stdout)";fi
+IDFileConverter -test -in IDFileConverter_1_input1.mascotXML -mz_file IDFileConverter_1_input2.mzML -out IDFileConverter_1_output.tmp -out_type idXML > TOPP_IDFileConverter_1.stdout 2> TOPP_IDFileConverter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_1.stdout)";fi
+IDFileConverter -test -in PepXMLFile_test.pepxml -mz_file PepXMLFile_test.mzML -mz_name PepXMLFile_test -out IDFileConverter_2_output.tmp -out_type idXML > TOPP_IDFileConverter_2.stdout 2> TOPP_IDFileConverter_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_2.stdout)";fi
+IDFileConverter -test -in IDFileConverter_3_input.protXML -out IDFileConverter_3_output.tmp -out_type idXML > TOPP_IDFileConverter_3.stdout 2> TOPP_IDFileConverter_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_3.stdout)";fi
+IDFileConverter -test -in IDFileConverter_1_input1.mascotXML -mz_file IDFileConverter_1_input2.mzML -out IDFileConverter_5_output.tmp -ini IDFileConverter_5_parameters.ini > TOPP_IDFileConverter_5.stdout 2> TOPP_IDFileConverter_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_5.stdout)";fi
+IDFileConverter -test -in IDFileConverter_6_input1.pepXML -mz_file IDFileConverter_1_input2.mzML -mz_name F025589.dat.mzML -out IDFileConverter_6_output.tmp -out_type idXML > TOPP_IDFileConverter_6.stdout 2> TOPP_IDFileConverter_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_6.stdout)";fi
+IDFileConverter -test -in IDFileConverter_7_input1.xml -out IDFileConverter_7_output.tmp -out_type idXML > TOPP_IDFileConverter_7.stdout 2> TOPP_IDFileConverter_7.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_7.stdout)";fi
+IDFileConverter -test -in IDFileConverter_8_input.mzid -out IDFileConverter_8_output.tmp -out_type idXML > TOPP_IDFileConverter_8.stdout 2> TOPP_IDFileConverter_8.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_8.stdout)";fi
+IDFileConverter -test -in IDFileConverter_9_input.idXML -out IDFileConverter_9_output.tmp -out_type mzid > TOPP_IDFileConverter_9.stdout 2> TOPP_IDFileConverter_9.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_9.stdout)";fi
+IDFileConverter -test -in IDFileConverter_10_input.pepXML -out IDFileConverter_10_output.tmp -out_type idXML > TOPP_IDFileConverter_10.stdout 2> TOPP_IDFileConverter_10.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_10.stdout)";fi
+IDFileConverter -test -in IDFileConverter_11_input.tsv -out IDFileConverter_11_output.tmp -out_type idXML > TOPP_IDFileConverter_11.stdout 2> TOPP_IDFileConverter_11.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_11 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_11.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_11.stdout)";fi
+IDFileConverter -test -in IDFileConverter_12_input.psms -out IDFileConverter_12_output.tmp -out_type idXML -score_type qvalue > TOPP_IDFileConverter_12.stdout 2> TOPP_IDFileConverter_12.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_12 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_12.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_12.stdout)";fi
+IDFileConverter -test -in IDFileConverter_12_input.psms -out IDFileConverter_13_output.tmp -out_type idXML -score_type PEP > TOPP_IDFileConverter_13.stdout 2> TOPP_IDFileConverter_13.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_13 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_13.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_13.stdout)";fi
+IDFileConverter -test -in IDFileConverter_12_input.psms -out IDFileConverter_14_output.tmp -out_type idXML -score_type score > TOPP_IDFileConverter_14.stdout 2> TOPP_IDFileConverter_14.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_14 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_14.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_14.stdout)";fi
+IDFileConverter -test -in MSGFPlusAdapter_1_out.mzid -out IDFileConverter_15_output.tmp -out_type idXML -mz_file spectra.mzML > TOPP_IDFileConverter_15.stdout 2> TOPP_IDFileConverter_15.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_15 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_15.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_15.stdout)";fi
+IDFileConverter -test -in IDFileConverter_16_input.pepXML -out IDFileConverter_16_output.tmp -out_type idXML > TOPP_IDFileConverter_16.stdout 2> TOPP_IDFileConverter_16.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_16 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_16.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_16.stdout)";fi
+IDFileConverter -test -in IDFileConverter_17_input.idXML -out IDFileConverter_17_output.tmp -out_type pepXML > TOPP_IDFileConverter_17.stdout 2> TOPP_IDFileConverter_17.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_17 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_17.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_17.stdout)";fi
+IDFileConverter -test -in IDFileConverter_18_input.idXML -out IDFileConverter_18_output.tmp -out_type pepXML > TOPP_IDFileConverter_18.stdout 2> TOPP_IDFileConverter_18.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_18 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_18.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_18.stdout)";fi
+IDFileConverter -test -in IDFileConverter_19_input.idXML -out IDFileConverter_19_output.tmp -out_type pepXML > TOPP_IDFileConverter_19.stdout 2> TOPP_IDFileConverter_19.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_19 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_19.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_19.stdout)";fi
+IDFileConverter -test -in IDFileConverter_20_input.idXML -out IDFileConverter_20_output.tmp -out_type pepXML > TOPP_IDFileConverter_20.stdout 2> TOPP_IDFileConverter_20.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_20 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_20.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_20.stdout)";fi
+IDFileConverter -test -in IDFileConverter_21_input.idXML -out_type idXML -out IDFileConverter_21_output.tmp -mz_file IDMapper_4_input.mzML > TOPP_IDFileConverter_21.stdout 2> TOPP_IDFileConverter_21.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_21 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_21.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_21.stdout)";fi
+IDFileConverter -test -in MSGFPlusAdapter_1_out.mzid -out IDFileConverter_22_output.tmp -out_type idXML -mz_file spectra.mzML -add_ionmatch_annotation 0.01 > TOPP_IDFileConverter_22.stdout 2> TOPP_IDFileConverter_22.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_22 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_22.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_22.stdout)";fi
+IDFileConverter -test -in IDFileConverter_23_input.mzid -out IDFileConverter_23_output.tmp -out_type idXML > TOPP_IDFileConverter_23.stdout 2> TOPP_IDFileConverter_23.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_23 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_23.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_23.stdout)";fi
+IDFileConverter -test -in IDFileConverter_24_input.pep.xml -out IDFileConverter_24_output.tmp -out_type idXML > TOPP_IDFileConverter_24.stdout 2> TOPP_IDFileConverter_24.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_24 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_24.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_24.stdout)";fi
+IDFileConverter -test -in IDFileConverter_25_input.idXML -out IDFileConverter_25_output.tmp -out_type pepXML > TOPP_IDFileConverter_25.stdout 2> TOPP_IDFileConverter_25.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_25 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_25.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_25.stdout)";fi
+IDFileConverter -test -in IDFileConverter_26_input.mzid -out IDFileConverter_26_output.tmp -out_type idXML > TOPP_IDFileConverter_26.stdout 2> TOPP_IDFileConverter_26.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFileConverter_26 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFileConverter_26.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFileConverter_26.stdout)";fi
+IDFilter -test -in IDFilter_1_input.idXML -out IDFilter_1_output.tmp -whitelist:proteins IDFilter_1_input.fas > TOPP_IDFilter_1.stdout 2> TOPP_IDFilter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_1.stdout)";fi
+IDFilter -test -in IDFilter_3_input.idXML -out IDFilter_3_output.tmp -blacklist:peptides IDFilter_3_2_input.idXML > TOPP_IDFilter_3.stdout 2> TOPP_IDFilter_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_3.stdout)";fi
+IDFilter -test -in IDFilter_4_input.idXML -out IDFilter_4_output.tmp -rt:p_value 0.08 > TOPP_IDFilter_4.stdout 2> TOPP_IDFilter_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_4.stdout)";fi
+IDFilter -test -in IDFilter_5_input.idXML -out IDFilter_5_output.tmp -score:pep 32 -score:prot 25 > TOPP_IDFilter_5.stdout 2> TOPP_IDFilter_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_5.stdout)";fi
+IDFilter -test -in IDFilter_5_input.idXML -out IDFilter_5a_output.tmp -score:pep 32 > TOPP_IDFilter_5a.stdout 2> TOPP_IDFilter_5a.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_5a failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_5a.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_5a.stdout)";fi
+IDFilter -test -in IDFilter_5_input.idXML -out IDFilter_5b_output.tmp -score:prot 25 > TOPP_IDFilter_5b.stdout 2> TOPP_IDFilter_5b.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_5b failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_5b.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_5b.stdout)";fi
+IDFilter -test -in IDFilter_5_input.idXML -out IDFilter_5c_output.tmp -score:prot 25 -delete_unreferenced_peptide_hits > TOPP_IDFilter_5c.stdout 2> TOPP_IDFilter_5c.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_5c failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_5c.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_5c.stdout)";fi
+IDFilter -test -in IDFilter_6_input.idXML -out IDFilter_6_output.tmp -best:n_peptide_hits 2 -best:n_protein_hits 10 > TOPP_IDFilter_6.stdout 2> TOPP_IDFilter_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_6.stdout)";fi
+IDFilter -test -in IDFilter_7_input.idXML -out IDFilter_7_output.tmp -remove_duplicate_psm > TOPP_IDFilter_7.stdout 2> TOPP_IDFilter_7.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_7.stdout)";fi
+IDFilter -test -in IDFilter_8_input.idXML -out IDFilter_8_output.tmp -precursor:rt 200:350 -precursor:mz 999:1000 > TOPP_IDFilter_8.stdout 2> TOPP_IDFilter_8.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_8.stdout)";fi
+IDFilter -test -in IDFilter_9_input.idXML -out IDFilter_9_output.tmp -score:pep 0.05 > TOPP_IDFilter_9.stdout 2> TOPP_IDFilter_9.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_9.stdout)";fi
+IDFilter -test -in IDFilter_10_input.idXML -out IDFilter_10_output.tmp -score:prot 0.3 -delete_unreferenced_peptide_hits > TOPP_IDFilter_10.stdout 2> TOPP_IDFilter_10.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_10.stdout)";fi
+IDFilter -test -in IDFilter_11_input.idXML -out IDFilter_11_output.tmp -remove_decoys -delete_unreferenced_peptide_hits > TOPP_IDFilter_11.stdout 2> TOPP_IDFilter_11.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_11 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_11.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_11.stdout)";fi
+IDFilter -test -in IDFilter_12_input.idXML -out IDFilter_12_output.tmp -in_silico_digestion:fasta IDFilter_12_input.fasta > TOPP_IDFilter_12.stdout 2> TOPP_IDFilter_12.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_12 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_12.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_12.stdout)";fi
+IDFilter -test -in IDFilter_13_input.idXML -out IDFilter_13_output.tmp -in_silico_digestion:fasta IDFilter_13_input.fasta -in_silico_digestion:missed_cleavages 1 > TOPP_IDFilter_13.stdout 2> TOPP_IDFilter_13.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_13 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_13.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_13.stdout)";fi
+IDFilter -test -in IDFilter_14_input.idXML -out IDFilter_14_output.tmp -in_silico_digestion:fasta IDFilter_14_input.fasta -in_silico_digestion:enzyme Trypsin/P -in_silico_digestion:missed_cleavages 1 > TOPP_IDFilter_14.stdout 2> TOPP_IDFilter_14.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_14 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_14.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_14.stdout)";fi
+IDFilter -test -in IDFilter_15_input.idXML -out IDFilter_15_output.tmp -in_silico_digestion:fasta IDFilter_15_input.fasta -in_silico_digestion:enzyme Trypsin/P -in_silico_digestion:missed_cleavages 1 -in_silico_digestion:specificity semi > TOPP_IDFilter_15.stdout 2> TOPP_IDFilter_15.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_15 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_15.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_15.stdout)";fi
+IDFilter -test -in IDFilter_16_input.idXML -out IDFilter_16_output.tmp -in_silico_digestion:fasta IDFilter_16_input.fasta -in_silico_digestion:enzyme Trypsin/P -in_silico_digestion:missed_cleavages 1 -in_silico_digestion:methionine_cleavage > TOPP_IDFilter_16.stdout 2> TOPP_IDFilter_16.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_16 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_16.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_16.stdout)";fi
+IDFilter -test -in IDFilter_missed_cleavages_input.idXML -out IDFilter_17_output.tmp -missed_cleavages:enzyme Lys-N -missed_cleavages:number_of_missed_cleavages :2 > TOPP_IDFilter_17.stdout 2> TOPP_IDFilter_17.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_17 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_17.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_17.stdout)";fi
+IDFilter -test -in IDFilter_missed_cleavages_input.idXML -out IDFilter_18_output.tmp -missed_cleavages:enzyme Lys-N -missed_cleavages:number_of_missed_cleavages 2: > TOPP_IDFilter_18.stdout 2> TOPP_IDFilter_18.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_18 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_18.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_18.stdout)";fi
+IDFilter -test -in IDFilter_missed_cleavages_input.idXML -out IDFilter_19_output.tmp -missed_cleavages:enzyme Lys-N -missed_cleavages:number_of_missed_cleavages 1:3 > TOPP_IDFilter_19.stdout 2> TOPP_IDFilter_19.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_19 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_19.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_19.stdout)";fi
+IDFilter -test -in IDFilter_missed_cleavages_input.idXML -out IDFilter_20_output.tmp -missed_cleavages:number_of_missed_cleavages 1:0 > TOPP_IDFilter_20.stdout 2> TOPP_IDFilter_20.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_20 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_20.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_20.stdout)";fi
+IDFilter -test -in IDFilter_16_input.idXML -out IDFilter_21_output.tmp -remove_peptide_hits_by_metavalue "calcMZ" "gt" "750.0" > TOPP_IDFilter_21.stdout 2> TOPP_IDFilter_21.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_21 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_21.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_21.stdout)";fi
+IDFilter -test -in IDFilter_16_input.idXML -out IDFilter_22_output.tmp -remove_peptide_hits_by_metavalue "end" "ne" "23" > TOPP_IDFilter_22.stdout 2> TOPP_IDFilter_22.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDFilter_22 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDFilter_22.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDFilter_22.stdout)";fi
+MapAlignerPoseClustering -test -ini MapAlignerPoseClustering_1_parameters.ini -in MapAlignerPoseClustering_1_input1.featureXML MapAlignerPoseClustering_1_input2.featureXML MapAlignerPoseClustering_1_input3.featureXML -out MapAlignerPoseClustering_1_output1.tmp MapAlignerPoseClustering_1_output2.tmp MapAlignerPoseClustering_1_output3.tmp -trafo_out MapAlignerPoseClustering_1_trafo1.tmp MapAlignerPoseClustering_1_trafo2.tmp MapAlignerPoseClustering_1_trafo3.tmp > TOPP_MapAlignerPoseClustering_1.stdout 2> TOPP_MapAlignerPoseClustering_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerPoseClustering_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerPoseClustering_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerPoseClustering_1.stdout)";fi
+MapAlignerPoseClustering -test -ini MapAlignerPoseClustering_2_parameters.ini -in MapAlignerPoseClustering_2_input1.mzML MapAlignerPoseClustering_2_input2.mzML MapAlignerPoseClustering_2_input3.mzML -out MapAlignerPoseClustering_2_output1.tmp MapAlignerPoseClustering_2_output2.tmp MapAlignerPoseClustering_2_output3.tmp > TOPP_MapAlignerPoseClustering_2.stdout 2> TOPP_MapAlignerPoseClustering_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerPoseClustering_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerPoseClustering_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerPoseClustering_2.stdout)";fi
+MapAlignerPoseClustering -test -ini MapAlignerPoseClustering_1_parameters.ini -in MapAlignerPoseClustering_1_input2.featureXML MapAlignerPoseClustering_1_input3.featureXML -out MapAlignerPoseClustering_3_output1.tmp MapAlignerPoseClustering_3_output2.tmp -reference:file MapAlignerPoseClustering_1_input1.featureXML > TOPP_MapAlignerPoseClustering_3.stdout 2> TOPP_MapAlignerPoseClustering_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerPoseClustering_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerPoseClustering_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerPoseClustering_3.stdout)";fi
+MapAlignerPoseClustering -test -ini MapAlignerPoseClustering_1_parameters.ini -in MapAlignerPoseClustering_1_input1.featureXML MapAlignerPoseClustering_1_input2.featureXML -trafo_out MapAlignerPoseClustering_4_trafo1.tmp MapAlignerPoseClustering_4_trafo2.tmp -reference:index 2 > TOPP_MapAlignerPoseClustering_4.stdout 2> TOPP_MapAlignerPoseClustering_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerPoseClustering_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerPoseClustering_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerPoseClustering_4.stdout)";fi
+MapAlignerIdentification -test -ini MapAlignerIdentification_parameters.ini -in MapAlignerIdentification_1_input1.featureXML MapAlignerIdentification_1_input2.featureXML -out MapAlignerIdentification_1_output1.tmp MapAlignerIdentification_1_output2.tmp > TOPP_MapAlignerIdentification_1.stdout 2> TOPP_MapAlignerIdentification_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerIdentification_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerIdentification_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerIdentification_1.stdout)";fi
+MapAlignerIdentification -test -ini MapAlignerIdentification_parameters.ini -in MapAlignerIdentification_1_input1.featureXML -out MapAlignerIdentification_2_output1.tmp -reference:file MapAlignerIdentification_1_input2.featureXML > TOPP_MapAlignerIdentification_2.stdout 2> TOPP_MapAlignerIdentification_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerIdentification_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerIdentification_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerIdentification_2.stdout)";fi
+MapAlignerIdentification -test -ini MapAlignerIdentification_parameters.ini -in MapAlignerIdentification_1_input2.featureXML MapAlignerIdentification_1_input1.featureXML -out MapAlignerIdentification_3_output1.tmp MapAlignerIdentification_3_output2.tmp -reference:index 1 > TOPP_MapAlignerIdentification_3.stdout 2> TOPP_MapAlignerIdentification_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerIdentification_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerIdentification_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerIdentification_3.stdout)";fi
+MapAlignerIdentification -test -ini MapAlignerIdentification_parameters.ini -in MapAlignerIdentification_1_input1.featureXML MapAlignerIdentification_1_input2.featureXML -out MapAlignerIdentification_4_output1.tmp MapAlignerIdentification_4_output2.tmp -reference:index 2 > TOPP_MapAlignerIdentification_4.stdout 2> TOPP_MapAlignerIdentification_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerIdentification_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerIdentification_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerIdentification_4.stdout)";fi
+MapAlignerIdentification -test -ini MapAlignerIdentification_parameters.ini -in MapAlignerIdentification_5_input1.consensusXML MapAlignerIdentification_5_input2.consensusXML -out MapAlignerIdentification_5_output1.tmp MapAlignerIdentification_5_output2.tmp > TOPP_MapAlignerIdentification_5.stdout 2> TOPP_MapAlignerIdentification_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerIdentification_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerIdentification_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerIdentification_5.stdout)";fi
+MapAlignerIdentification -test -ini MapAlignerIdentification_parameters.ini -in MapAlignerIdentification_1_input1.featureXML -trafo_out MapAlignerIdentification_6_output1.tmp -reference:file MapAlignerIdentification_1_input2.featureXML > TOPP_MapAlignerIdentification_6.stdout 2> TOPP_MapAlignerIdentification_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerIdentification_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerIdentification_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerIdentification_6.stdout)";fi
+MapAlignerSpectrum -test -ini MapAlignerSpectrum_parameters.ini -in MapAlignerSpectrum_1_input1.mzML MapAlignerSpectrum_1_input2.mzML MapAlignerSpectrum_1_input3.mzML -out MapAlignerSpectrum_1_output1.tmp MapAlignerSpectrum_1_output2.tmp MapAlignerSpectrum_1_output3.tmp > TOPP_MapAlignerSpectrum_1.stdout 2> TOPP_MapAlignerSpectrum_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerSpectrum_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerSpectrum_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerSpectrum_1.stdout)";fi
+MapAlignerTreeGuided -test -ini MapAlignerTreeGuided_parameters.ini -in MapAlignerTreeGuided_1_input1.featureXML MapAlignerTreeGuided_1_input2.featureXML MapAlignerTreeGuided_1_input3.featureXML -out MapAlignerTreeGuided_1_output1.tmp MapAlignerTreeGuided_1_output2.tmp MapAlignerTreeGuided_1_output3.tmp > TOPP_MapAlignerTreeGuided_1.stdout 2> TOPP_MapAlignerTreeGuided_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerTreeGuided_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerTreeGuided_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerTreeGuided_1.stdout)";fi
+MapAlignerTreeGuided -test -ini MapAlignerTreeGuided_parameters.ini -in MapAlignerTreeGuided_1_input1.featureXML MapAlignerTreeGuided_1_input2.featureXML MapAlignerTreeGuided_1_input3.featureXML -trafo_out MapAlignerTreeGuided_2_output1.tmp MapAlignerTreeGuided_2_output2.tmp MapAlignerTreeGuided_2_output3.tmp > TOPP_MapAlignerTreeGuided_2.stdout 2> TOPP_MapAlignerTreeGuided_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapAlignerTreeGuided_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapAlignerTreeGuided_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapAlignerTreeGuided_2.stdout)";fi
+MapRTTransformer -test -in MapRTTransformer_1_input.featureXML -trafo_in MapRTTransformer_trafo_linear.trafoXML -out MapRTTransformer_1_output.tmp > TOPP_MapRTTransformer_1.stdout 2> TOPP_MapRTTransformer_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapRTTransformer_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapRTTransformer_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapRTTransformer_1.stdout)";fi
+MapRTTransformer -test -in MapRTTransformer_2_input.mzML -trafo_in MapRTTransformer_trafo_linear.trafoXML -out MapRTTransformer_2_output.tmp > TOPP_MapRTTransformer_2.stdout 2> TOPP_MapRTTransformer_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapRTTransformer_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapRTTransformer_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapRTTransformer_2.stdout)";fi
+MapRTTransformer -test -invert -trafo_in MapAlignerPoseClustering_1_trafo2.trafoXML -trafo_out MapRTTransformer_3_output.tmp > TOPP_MapRTTransformer_3.stdout 2> TOPP_MapRTTransformer_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapRTTransformer_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapRTTransformer_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapRTTransformer_3.stdout)";fi
+MapRTTransformer -test -in MapRTTransformer_4_input.chrom.mzML -trafo_in MapRTTransformer_trafo_linear.trafoXML -out MapRTTransformer_4_output.tmp > TOPP_MapRTTransformer_4.stdout 2> TOPP_MapRTTransformer_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapRTTransformer_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapRTTransformer_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapRTTransformer_4.stdout)";fi
+MapRTTransformer -test -in MapRTTransformer_1_input.featureXML -trafo_in MapRTTransformer_trafo_none.trafoXML -out MapRTTransformer_5_output.tmp > TOPP_MapRTTransformer_5.stdout 2> TOPP_MapRTTransformer_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapRTTransformer_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapRTTransformer_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapRTTransformer_5.stdout)";fi
+MapRTTransformer -test -in MapRTTransformer_1_input.featureXML -trafo_in MapRTTransformer_trafo_linear.trafoXML -out MapRTTransformer_6_output.tmp -store_original_rt > TOPP_MapRTTransformer_6.stdout 2> TOPP_MapRTTransformer_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MapRTTransformer_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MapRTTransformer_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MapRTTransformer_6.stdout)";fi
+MetaProSIP -test -in_mzML MetaProSIP_1_input.mzML -in_fasta MetaProSIP_1_input.fasta -in_featureXML MetaProSIP_1_input.featureXML -out_csv MetaProSIP_1_output_1.tmp -out_peptide_centric_csv MetaProSIP_1_output_2.tmp > TOPP_MetaProSIP_1.stdout 2> TOPP_MetaProSIP_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MetaProSIP_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MetaProSIP_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MetaProSIP_1.stdout)";fi
+MascotAdapter -test -ini MascotAdapter_1_parameters.ini -mascot_in -in MascotAdapter_1_input.mzData > TOPP_MascotAdapter_1.stdout 2> TOPP_MascotAdapter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MascotAdapter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MascotAdapter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MascotAdapter_1.stdout)";fi
+MascotAdapter -test -in MascotAdapter_2_input.mascotXML -out MascotAdapter_2_output.tmp -mascot_out > TOPP_MascotAdapter_2.stdout 2> TOPP_MascotAdapter_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MascotAdapter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MascotAdapter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MascotAdapter_2.stdout)";fi
+MSstatsConverter -test -in MSstatsConverter_1_in.consensusXML -retention_time_summarization_method max -in_design MSstatsConverter_1_design.tsv -out MSstatsConverter_1_out.tmp > TOPP_MSstatsConverter_1.stdout 2> TOPP_MSstatsConverter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MSstatsConverter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MSstatsConverter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MSstatsConverter_1.stdout)";fi
+MSstatsConverter -test -in MSstatsConverter_2_in.consensusXML -method "ISO" -retention_time_summarization_method manual -in_design MSstatsConverter_2_design.tsv -out MSstatsConverter_2_out.tmp -msstats_bioreplicate MSstats_BioReplicate -msstats_condition MSstats_Condition -msstats_mixture MSstats_Mixture > TOPP_MSstatsConverter_2.stdout 2> TOPP_MSstatsConverter_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MSstatsConverter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MSstatsConverter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MSstatsConverter_2.stdout)";fi
+MSstatsConverter -test -in MSstatsConverter_3_in.consensusXML -method "ISO" -retention_time_summarization_method manual -in_design MSstatsConverter_3_design.tsv -out MSstatsConverter_3_out.tmp -msstats_bioreplicate MSstats_BioReplicate -msstats_condition MSstats_Condition -msstats_mixture MSstats_Mixture > TOPP_MSstatsConverter_3.stdout 2> TOPP_MSstatsConverter_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MSstatsConverter_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MSstatsConverter_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MSstatsConverter_3.stdout)";fi
+SpecLibSearcher -test -ini SpecLibSearcher_1_parameters.ini -in SpecLibSearcher_1.mzML -lib SpecLibSearcher_1.MSP -out SpecLibSearcher_1.tmp > TOPP_SpecLibSearcher_1.stdout 2> TOPP_SpecLibSearcher_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SpecLibSearcher_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SpecLibSearcher_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SpecLibSearcher_1.stdout)";fi
+OpenSwathAssayGenerator -test -in OpenSwathAssayGenerator_input.TraML -out OpenSwathAssayGenerator_output.TraML.tmp -out_type TraML -min_transitions 6 -max_transitions 6 -allowed_fragment_types b,y -allowed_fragment_charges 2,3 -enable_detection_specific_losses > TOPP_OpenSwathAssayGenerator_test_1.stdout 2> TOPP_OpenSwathAssayGenerator_test_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAssayGenerator_test_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAssayGenerator_test_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAssayGenerator_test_1.stdout)";fi
+OpenSwathAssayGenerator -test -in OpenSwathAssayGenerator_input_2.TraML -out OpenSwathAssayGenerator_output_2.TraML.tmp -out_type TraML -allowed_fragment_charges 1,2,3,4 -enable_ipf -unimod_file OpenSwathAssayGenerator_input_2_unimod.xml > TOPP_OpenSwathAssayGenerator_test_2.stdout 2> TOPP_OpenSwathAssayGenerator_test_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAssayGenerator_test_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAssayGenerator_test_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAssayGenerator_test_2.stdout)";fi
+OpenSwathAssayGenerator -test -in OpenSwathAssayGenerator_input_2.TraML -out OpenSwathAssayGenerator_output_3.TraML.tmp -out_type TraML -allowed_fragment_charges 1,2,3,4 -enable_ipf -unimod_file OpenSwathAssayGenerator_input_3_unimod.xml > TOPP_OpenSwathAssayGenerator_test_3.stdout 2> TOPP_OpenSwathAssayGenerator_test_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAssayGenerator_test_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAssayGenerator_test_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAssayGenerator_test_3.stdout)";fi
+OpenSwathDecoyGenerator -test -in OpenSwathDecoyGenerator_input.TraML -out OpenSwathDecoyGenerator.TraML.tmp -out_type TraML -method pseudo-reverse -separate -switchKR false > TOPP_OpenSwathDecoyGenerator_test_1.stdout 2> TOPP_OpenSwathDecoyGenerator_test_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathDecoyGenerator_test_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathDecoyGenerator_test_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathDecoyGenerator_test_1.stdout)";fi
+OpenSwathDecoyGenerator -test -in OpenSwathDecoyGenerator_input_2.TraML -out OpenSwathDecoyGenerator_2.TraML.tmp -out_type TraML -method pseudo-reverse -product_mz_threshold 0.8 -switchKR false > TOPP_OpenSwathDecoyGenerator_test_2.stdout 2> TOPP_OpenSwathDecoyGenerator_test_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathDecoyGenerator_test_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathDecoyGenerator_test_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathDecoyGenerator_test_2.stdout)";fi
+OpenSwathDecoyGenerator -test -in OpenSwathDecoyGenerator_input_3.TraML -out OpenSwathDecoyGenerator_3.TraML.tmp -out_type TraML -method pseudo-reverse -separate -switchKR false > TOPP_OpenSwathDecoyGenerator_test_3.stdout 2> TOPP_OpenSwathDecoyGenerator_test_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathDecoyGenerator_test_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathDecoyGenerator_test_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathDecoyGenerator_test_3.stdout)";fi
+OpenSwathDecoyGenerator -test -in OpenSwathDecoyGenerator_input_4.tsv -out OpenSwathDecoyGenerator_4.TraML.tmp -out_type TraML -method pseudo-reverse -separate -switchKR true -enable_detection_unspecific_losses -enable_detection_specific_losses -min_decoy_fraction 0.4 > TOPP_OpenSwathDecoyGenerator_test_4.stdout 2> TOPP_OpenSwathDecoyGenerator_test_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathDecoyGenerator_test_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathDecoyGenerator_test_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathDecoyGenerator_test_4.stdout)";fi
+TargetedFileConverter -test -in ConvertTSVToTraML_1_input.tsv -out ConvertTSVToTraML_output.TraML.tmp -out_type TraML > TOPP_ConvertTSVToTraML_test_1.stdout 2> TOPP_ConvertTSVToTraML_test_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConvertTSVToTraML_test_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConvertTSVToTraML_test_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConvertTSVToTraML_test_1.stdout)";fi
+TargetedFileConverter -test -in ConvertTSVToTraML_2_input.tsv -out ConvertTSVToTraML_2_output.TraML.tmp -algorithm:retentionTimeInterpretation minutes -out_type TraML > TOPP_ConvertTSVToTraML_test_2.stdout 2> TOPP_ConvertTSVToTraML_test_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConvertTSVToTraML_test_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConvertTSVToTraML_test_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConvertTSVToTraML_test_2.stdout)";fi
+TargetedFileConverter -test -in ConvertTSVToTraML_2_input.tsv -out ConvertTSVToTraML_3_output.TraML.tmp -algorithm:retentionTimeInterpretation seconds -out_type TraML > TOPP_ConvertTSVToTraML_test_3.stdout 2> TOPP_ConvertTSVToTraML_test_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConvertTSVToTraML_test_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConvertTSVToTraML_test_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConvertTSVToTraML_test_3.stdout)";fi
+TargetedFileConverter -test -in ConvertTSVToTraML_4_input.mrm -out ConvertTSVToTraML_4_output.TraML.tmp -out_type TraML > TOPP_ConvertTSVToTraML_test_4.stdout 2> TOPP_ConvertTSVToTraML_test_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConvertTSVToTraML_test_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConvertTSVToTraML_test_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConvertTSVToTraML_test_4.stdout)";fi
+TargetedFileConverter -test -in ConvertTSVToTraML_5_input.tsv -out ConvertTSVToTraML_5_output.TraML.tmp -out_type TraML > TOPP_ConvertTSVToTraML_test_5.stdout 2> TOPP_ConvertTSVToTraML_test_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConvertTSVToTraML_test_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConvertTSVToTraML_test_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConvertTSVToTraML_test_5.stdout)";fi
+TargetedFileConverter -test -in ConvertTSVToTraML_6_input.tsv -out ConvertTSVToTraML_6_output.TraML.tmp -out_type TraML > TOPP_ConvertTSVToTraML_test_6.stdout 2> TOPP_ConvertTSVToTraML_test_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConvertTSVToTraML_test_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConvertTSVToTraML_test_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConvertTSVToTraML_test_6.stdout)";fi
+TargetedFileConverter -test -in ConvertTSVToTraML_7_input_Skyline.tsv -out ConvertTSVToTraML_7_output.TraML.tmp -out_type TraML > TOPP_ConvertTSVToTraML_test_7.stdout 2> TOPP_ConvertTSVToTraML_test_7.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConvertTSVToTraML_test_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConvertTSVToTraML_test_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConvertTSVToTraML_test_7.stdout)";fi
+TargetedFileConverter -test -in TargetedFileConverter_1_input.TraML -out TargetedFileConverter_1_output.pqp.tmp -out_type pqp > TOPP_TargetedFileConverter_test_1_prepare.stdout 2> TOPP_TargetedFileConverter_test_1_prepare.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_1_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_1_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_1_prepare.stdout)";fi
+TargetedFileConverter -test -in TargetedFileConverter_1_output.pqp.tmp -in_type pqp -out TargetedFileConverter_1_output.TraML.tmp -out_type TraML > TOPP_TargetedFileConverter_test_1.stdout 2> TOPP_TargetedFileConverter_test_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_1.stdout)";fi
+TargetedFileConverter -test -in TargetedFileConverter_1_output.pqp.tmp -in_type pqp -out TargetedFileConverter_2_output.TraML.tmp -out_type TraML -legacy_traml_id > TOPP_TargetedFileConverter_test_2.stdout 2> TOPP_TargetedFileConverter_test_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_2.stdout)";fi
+TargetedFileConverter -test -in TargetedFileConverter_3_input.TraML -out TargetedFileConverter_3_output.pqp.tmp -out_type pqp > TOPP_TargetedFileConverter_test_3_prepare.stdout 2> TOPP_TargetedFileConverter_test_3_prepare.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_3_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_3_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_3_prepare.stdout)";fi
+TargetedFileConverter -test -in TargetedFileConverter_3_output.pqp.tmp -in_type pqp -out TargetedFileConverter_3_output.TraML.tmp -out_type TraML > TOPP_TargetedFileConverter_test_3.stdout 2> TOPP_TargetedFileConverter_test_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_3.stdout)";fi
+TargetedFileConverter -test -in TargetedFileConverter_3_output.pqp.tmp -in_type pqp -out TargetedFileConverter_4_output.TraML.tmp -out_type TraML -legacy_traml_id > TOPP_TargetedFileConverter_test_4.stdout 2> TOPP_TargetedFileConverter_test_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_4.stdout)";fi
+TargetedFileConverter -test -in TargetedFileConverter_10_input.pqp -out TargetedFileConverter_10_output.TraML.tmp -out_type TraML -legacy_traml_id > TOPP_TargetedFileConverter_test_10_prepare.stdout 2> TOPP_TargetedFileConverter_test_10_prepare.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_10_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_10_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_10_prepare.stdout)";fi
+TargetedFileConverter -test -in TargetedFileConverter_10_output.TraML.tmp -in_type TraML -out TargetedFileConverter_10_output.tsv.tmp -out_type tsv > TOPP_TargetedFileConverter_test_10.stdout 2> TOPP_TargetedFileConverter_test_10.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_10.stdout)";fi
+TargetedFileConverter -test -in TargetedFileConverter_11_input.TraML -out TargetedFileConverter_11_output.pqp.tmp -out_type pqp > TOPP_TargetedFileConverter_test_11_prepare.stdout 2> TOPP_TargetedFileConverter_test_11_prepare.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_11_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_11_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_11_prepare.stdout)";fi
+TargetedFileConverter -test -in TargetedFileConverter_11_output.pqp.tmp -in_type pqp -out TargetedFileConverter_11_output.TraML.tmp -out_type TraML > TOPP_TargetedFileConverter_test_11.stdout 2> TOPP_TargetedFileConverter_test_11.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_11 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_11.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_11.stdout)";fi
+TargetedFileConverter -algorithm:override_group_label_check -test -in TargetedFileConverter_8_input.tsv -out TargetedFileConverter_8_output.TraML.tmp -out_type TraML > TOPP_TargetedFileConverter_test_8_prepare.stdout 2> TOPP_TargetedFileConverter_test_8_prepare.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_8_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_8_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_8_prepare.stdout)";fi
+TargetedFileConverter -algorithm:override_group_label_check -test -in TargetedFileConverter_8_output.TraML.tmp -in_type TraML -out TargetedFileConverter_8_output.tsv.tmp -out_type tsv > TOPP_TargetedFileConverter_test_8.stdout 2> TOPP_TargetedFileConverter_test_8.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_8.stdout)";fi
+TargetedFileConverter -algorithm:override_group_label_check -test -in TargetedFileConverter_9_input.TraML -out TargetedFileConverter_9_output.pqp.tmp -out_type pqp > TOPP_TargetedFileConverter_test_9_prepare.stdout 2> TOPP_TargetedFileConverter_test_9_prepare.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_9_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_9_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_9_prepare.stdout)";fi
+TargetedFileConverter -algorithm:override_group_label_check -test -in TargetedFileConverter_9_output.pqp.tmp -in_type pqp -out TargetedFileConverter_9_output.TraML.tmp -out_type TraML > TOPP_TargetedFileConverter_test_9.stdout 2> TOPP_TargetedFileConverter_test_9.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_9.stdout)";fi
+TargetedFileConverter -test -in ConvertTSVToTraML_output.TraML -out ConvertTraMLToTSV_output.tmp.tsv -out_type tsv > TOPP_TargetedFileConverter_test_5.stdout 2> TOPP_TargetedFileConverter_test_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_5.stdout)";fi
+TargetedFileConverter -algorithm:override_group_label_check -test -in TargetedFileConverter_12_input.TraML -out TargetedFileConverter_12_output.pqp.tmp -out_type pqp > TOPP_TargetedFileConverter_test_12_prepare.stdout 2> TOPP_TargetedFileConverter_test_12_prepare.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_12_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_12_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_12_prepare.stdout)";fi
+TargetedFileConverter -algorithm:override_group_label_check -test -in TargetedFileConverter_12_output.pqp.tmp -in_type pqp -out TargetedFileConverter_12_output.TraML.tmp -out_type TraML > TOPP_TargetedFileConverter_test_12.stdout 2> TOPP_TargetedFileConverter_test_12.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_12 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_12.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_12.stdout)";fi
+TargetedFileConverter -test -in TargetedFileConverter_12_input.tsv -out TargetedFileConverter_13_output.TraML.tmp -out_type TraML > TOPP_TargetedFileConverter_test_13.stdout 2> TOPP_TargetedFileConverter_test_13.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_13 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_13.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_13.stdout)";fi
+TargetedFileConverter -test -in ConvertTSVToTraML_5_output.TraML -out ConvertTraMLToTSV_output_2.tmp.tsv -out_type tsv > TOPP_TargetedFileConverter_test_6.stdout 2> TOPP_TargetedFileConverter_test_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_6.stdout)";fi
+TargetedFileConverter -test -in ConvertTraMLToTSV_output_2.tmp.tsv -in_type tsv -out ConvertTraMLToTSV_output_2.tsv.back.tmp -out_type TraML > TOPP_TargetedFileConverter_test_6_convert_back.stdout 2> TOPP_TargetedFileConverter_test_6_convert_back.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TargetedFileConverter_test_6_convert_back failed'; >&2 echo -e "stderr:\n$(cat TOPP_TargetedFileConverter_test_6_convert_back.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TargetedFileConverter_test_6_convert_back.stdout)";fi
+MRMMapper -in MRMMapping_input.chrom.mzML -tr MRMMapping_input.TraML -out MRMMapping_output_1.chrom.mzML.tmp -test -algorithm:precursor_tolerance 0.3 -algorithm:product_tolerance 0.3 > TOPP_MRMMapper_test_1.stdout 2> TOPP_MRMMapper_test_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MRMMapper_test_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MRMMapper_test_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MRMMapper_test_1.stdout)";fi
+MRMMapper -in MRMMapping_input.chrom.mzML -tr MRMMapping_input_2.TraML -out MRMMapping_output_2.chrom.mzML.tmp -test -algorithm:precursor_tolerance 0.01 -algorithm:product_tolerance 0.01 > TOPP_MRMMapper_test_2.stdout 2> TOPP_MRMMapper_test_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MRMMapper_test_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MRMMapper_test_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MRMMapper_test_2.stdout)";fi
+OpenSwathFeatureXMLToTSV -in OpenSwathFeatureXMLToTSV_input.featureXML -tr OpenSwathFeatureXMLToTSV_input.TraML -out OpenSwathFeatureXMLToTSV_output.short.csv.tmp -short_format -test > TOPP_OpenSwathFeatureXMLToTSV_test_1.stdout 2> TOPP_OpenSwathFeatureXMLToTSV_test_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathFeatureXMLToTSV_test_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathFeatureXMLToTSV_test_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathFeatureXMLToTSV_test_1.stdout)";fi
+OpenSwathFeatureXMLToTSV -in OpenSwathFeatureXMLToTSV_input.featureXML -tr OpenSwathFeatureXMLToTSV_input.TraML -out OpenSwathFeatureXMLToTSV_output.long.csv.tmp -test > TOPP_OpenSwathFeatureXMLToTSV_test_2.stdout 2> TOPP_OpenSwathFeatureXMLToTSV_test_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathFeatureXMLToTSV_test_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathFeatureXMLToTSV_test_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathFeatureXMLToTSV_test_2.stdout)";fi
+OpenSwathFeatureXMLToTSV -in OpenSwathFeatureXMLToTSV_input.featureXML -tr OpenSwathFeatureXMLToTSV_input.TraML -out OpenSwathFeatureXMLToTSV_3_output.short.csv.tmp -short_format -best_scoring_peptide main_var_xx_lda_prelim_score -test > TOPP_OpenSwathFeatureXMLToTSV_test_3.stdout 2> TOPP_OpenSwathFeatureXMLToTSV_test_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathFeatureXMLToTSV_test_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathFeatureXMLToTSV_test_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathFeatureXMLToTSV_test_3.stdout)";fi
+OpenSwathChromatogramExtractor -in OpenSwathChromatogramExtractor_input.mzML -tr OpenSwathChromatogramExtractor_input.TraML -out OpenSwathChromatogramExtractor_output.mzML.tmp -test > TOPP_OpenSwathChromatogramExtractor_test_1.stdout 2> TOPP_OpenSwathChromatogramExtractor_test_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathChromatogramExtractor_test_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathChromatogramExtractor_test_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathChromatogramExtractor_test_1.stdout)";fi
+OpenSwathChromatogramExtractor -in OpenSwathChromatogramExtractor_input.mzML -tr OpenSwathChromatogramExtractor_input.TraML -rt_norm OpenSwathChromatogramExtractor_input.trafoXML -out OpenSwathChromatogramExtractor_output_2.mzML.tmp -test -rt_window 50 > TOPP_OpenSwathChromatogramExtractor_test_2.stdout 2> TOPP_OpenSwathChromatogramExtractor_test_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathChromatogramExtractor_test_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathChromatogramExtractor_test_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathChromatogramExtractor_test_2.stdout)";fi
+OpenSwathChromatogramExtractor -in OpenSwathChromatogramExtractor_input.mzML -tr OpenSwathChromatogramExtractor_input.TraML -out OpenSwathChromatogramExtractor_output_3.mzML.tmp -test -extract_MS1 > TOPP_OpenSwathChromatogramExtractor_test_3.stdout 2> TOPP_OpenSwathChromatogramExtractor_test_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathChromatogramExtractor_test_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathChromatogramExtractor_test_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathChromatogramExtractor_test_3.stdout)";fi
+OpenSwathChromatogramExtractor -in OpenSwathChromatogramExtractor_4_input.mzML -tr OpenSwathChromatogramExtractor_4_input.TraML -out OpenSwathChromatogramExtractor_output_4.mzML.tmp -ion_mobility_window 0.05 -is_swath -test > TOPP_OpenSwathChromatogramExtractor_test_4.stdout 2> TOPP_OpenSwathChromatogramExtractor_test_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathChromatogramExtractor_test_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathChromatogramExtractor_test_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathChromatogramExtractor_test_4.stdout)";fi
+OpenSwathChromatogramExtractor -in OpenSwathChromatogramExtractor_input.mzML -tr OpenSwathChromatogramExtractor_5_input.TraML -out OpenSwathChromatogramExtractor_5_output.mzML.tmp -test -extract_MS1 > TOPP_OpenSwathChromatogramExtractor_test_5.stdout 2> TOPP_OpenSwathChromatogramExtractor_test_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathChromatogramExtractor_test_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathChromatogramExtractor_test_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathChromatogramExtractor_test_5.stdout)";fi
+OpenSwathAnalyzer -in OpenSwathAnalyzer_1_input_chrom.mzML -tr OpenSwathAnalyzer_1_input.TraML -out OpenSwathAnalyzer_1_output.featureXML.tmp -rt_norm OpenSwathAnalyzer_input.trafoXML -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width 40.0 -algorithm:TransitionGroupPicker:PeakPickerMRM:method legacy -test > TOPP_OpenSwathAnalyzer_test_1.stdout 2> TOPP_OpenSwathAnalyzer_test_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_1.stdout)";fi
+OpenSwathAnalyzer -in OpenSwathAnalyzer_1_input_chrom.mzML -tr OpenSwathAnalyzer_1_input.TraML -out OpenSwathAnalyzer_2_output.featureXML.tmp -swath_files OpenSwathAnalyzer_2_swathfile.mzML -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width 40.0 -algorithm:TransitionGroupPicker:PeakPickerMRM:method legacy -test > TOPP_OpenSwathAnalyzer_test_2.stdout 2> TOPP_OpenSwathAnalyzer_test_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_2.stdout)";fi
+OpenSwathAnalyzer -in OpenSwathAnalyzer_1_input_chrom.mzML -tr OpenSwathAnalyzer_mod_input.TraML -out OpenSwathAnalyzer_5_output.featureXML.tmp -swath_files OpenSwathAnalyzer_2_swathfile.mzML -ini OpenSwathAnalyzer_5.ini -test > TOPP_OpenSwathAnalyzer_test_5_mod.stdout 2> TOPP_OpenSwathAnalyzer_test_5_mod.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_5_mod failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_5_mod.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_5_mod.stdout)";fi
+OpenSwathAnalyzer -in OpenSwathAnalyzer_1_input_chrom.mzML -tr OpenSwathAnalyzer_1_input.TraML -out OpenSwathAnalyzer_6_output.featureXML.tmp -swath_files OpenSwathAnalyzer_2_swathfile.mzML -ini OpenSwathAnalyzer_5.ini -test > TOPP_OpenSwathAnalyzer_test_6_nomod.stdout 2> TOPP_OpenSwathAnalyzer_test_6_nomod.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_6_nomod failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_6_nomod.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_6_nomod.stdout)";fi
+OpenSwathAnalyzer -in OpenSwathAnalyzer_1_input_chrom.mzML -tr OpenSwathAnalyzer_1_input.TraML -out OpenSwathAnalyzer_7_output.featureXML.tmp -ini OpenSwathAnalyzer_7_backgroundSubtraction.ini -test > TOPP_OpenSwathAnalyzer_test_7_backgroundSubtraction.stdout 2> TOPP_OpenSwathAnalyzer_test_7_backgroundSubtraction.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_7_backgroundSubtraction failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_7_backgroundSubtraction.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_7_backgroundSubtraction.stdout)";fi
+OpenSwathAnalyzer -in OpenSwathAnalyzer_1_input_chrom.mzML -tr OpenSwathAnalyzer_1_input.TraML -out OpenSwathAnalyzer_8_output.featureXML.tmp -rt_norm OpenSwathAnalyzer_input.trafoXML -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width 40.0 -algorithm:TransitionGroupPicker:PeakPickerMRM:method legacy -algorithm:Scores:use_ms1_mi -algorithm:Scores:use_mi_score -algorithm:Scores:use_total_mi_score -test > TOPP_OpenSwathAnalyzer_test_8.stdout 2> TOPP_OpenSwathAnalyzer_test_8.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_8.stdout)";fi
+OpenSwathAnalyzer -in OpenSwathAnalyzer_1_input_chrom.mzML -tr OpenSwathAnalyzer_1_input.TraML -out OpenSwathAnalyzer_9_output.featureXML.tmp -rt_norm OpenSwathAnalyzer_input.trafoXML -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width 40.0 -algorithm:TransitionGroupPicker:PeakPickerMRM:method legacy -algorithm:Scores:use_mi_score -test > TOPP_OpenSwathAnalyzer_test_9.stdout 2> TOPP_OpenSwathAnalyzer_test_9.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_9.stdout)";fi
+OpenSwathAnalyzer -in OpenSwathAnalyzer_1_input_chrom.mzML -tr OpenSwathAnalyzer_1_input.TraML -out OpenSwathAnalyzer_10_output.featureXML.tmp -rt_norm OpenSwathAnalyzer_input.trafoXML -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width 40.0 -algorithm:TransitionGroupPicker:PeakPickerMRM:method legacy -algorithm:Scores:use_mi_score -algorithm:Scores:use_total_mi_score -test > TOPP_OpenSwathAnalyzer_test_10.stdout 2> TOPP_OpenSwathAnalyzer_test_10.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_10.stdout)";fi
+OpenSwathAnalyzer -in OpenSwathAnalyzer_1_input_chrom.mzML -tr OpenSwathAnalyzer_1_input.TraML -out OpenSwathAnalyzer_11_output.featureXML.tmp -rt_norm OpenSwathAnalyzer_input.trafoXML -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width 40.0 -algorithm:TransitionGroupPicker:PeakPickerMRM:method legacy -algorithm:Scores:use_total_mi_score -test > TOPP_OpenSwathAnalyzer_test_11.stdout 2> TOPP_OpenSwathAnalyzer_test_11.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_11 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_11.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_11.stdout)";fi
+OpenSwathRTNormalizer -in OpenSwathRTNormalizer_1_input.mzML -tr OpenSwathRTNormalizer_1_input.TraML -out OpenSwathRTNormalizer_1_output.trafoXML.tmp -test > TOPP_OpenSwathRTNormalizer_test_1.stdout 2> TOPP_OpenSwathRTNormalizer_test_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathRTNormalizer_test_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathRTNormalizer_test_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathRTNormalizer_test_1.stdout)";fi
+OpenSwathRTNormalizer -in OpenSwathRTNormalizer_1_input.mzML -tr OpenSwathRTNormalizer_1_input.TraML -out OpenSwathRTNormalizer_3_output.trafoXML.tmp -test -estimateBestPeptides -peptideEstimation:NrRTBins 3 -peptideEstimation:MinBinsFilled 3 > TOPP_OpenSwathRTNormalizer_test_3.stdout 2> TOPP_OpenSwathRTNormalizer_test_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathRTNormalizer_test_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathRTNormalizer_test_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathRTNormalizer_test_3.stdout)";fi
+OpenSwathRTNormalizer -in OpenSwathRTNormalizer_1_input.mzML -tr OpenSwathRTNormalizer_1_input.TraML -out OpenSwathRTNormalizer_4_output.trafoXML.tmp -test -RTNormalization:outlierMethod iter_residual > TOPP_OpenSwathRTNormalizer_test_4.stdout 2> TOPP_OpenSwathRTNormalizer_test_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathRTNormalizer_test_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathRTNormalizer_test_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathRTNormalizer_test_4.stdout)";fi
+OpenSwathConfidenceScoring -test -in OpenSwathFeatureXMLToTSV_input.featureXML -lib OpenSwathFeatureXMLToTSV_input.TraML -trafo OpenSwathConfidenceScoring_1_input.trafoXML -transitions 2 -decoys 1 -out OpenSwathConfidenceScoring_1_output.tmp > TOPP_OpenSwathConfidenceScoring_1.stdout 2> TOPP_OpenSwathConfidenceScoring_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathConfidenceScoring_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathConfidenceScoring_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathConfidenceScoring_1.stdout)";fi
+OpenSwathMzMLFileCacher -in OpenSwathMzMLFileCacher_1_input.mzML -out OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML -test > TOPP_OpenSwathMzMLFileCacher_test_1_step1.stdout 2> TOPP_OpenSwathMzMLFileCacher_test_1_step1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathMzMLFileCacher_test_1_step1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_1_step1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_1_step1.stdout)";fi
+OpenSwathMzMLFileCacher -in OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML -out OpenSwathMzMLFileCacher_1_output.tmp.mzML -convert_back -test > TOPP_OpenSwathMzMLFileCacher_test_1_step2.stdout 2> TOPP_OpenSwathMzMLFileCacher_test_1_step2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathMzMLFileCacher_test_1_step2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_1_step2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_1_step2.stdout)";fi
+OpenSwathMzMLFileCacher -in OpenSwathMzMLFileCacher_2_input.chrom.mzML -out OpenSwathMzMLFileCacher_2_input.chrom.cached.tmp.mzML -test > TOPP_OpenSwathMzMLFileCacher_test_2_step1.stdout 2> TOPP_OpenSwathMzMLFileCacher_test_2_step1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathMzMLFileCacher_test_2_step1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_2_step1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_2_step1.stdout)";fi
+OpenSwathMzMLFileCacher -in OpenSwathMzMLFileCacher_2_input.chrom.cached.tmp.mzML -out OpenSwathMzMLFileCacher_2_output.chrom.tmp.mzML -convert_back -test > TOPP_OpenSwathMzMLFileCacher_test_2_step2.stdout 2> TOPP_OpenSwathMzMLFileCacher_test_2_step2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathMzMLFileCacher_test_2_step2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_2_step2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_2_step2.stdout)";fi
+OpenSwathMzMLFileCacher -in OpenSwathMzMLFileCacher_1_input.mzML -out OpenSwathMzMLFileCacher_3_input.tmp.sqMass -test -lossy_compression true -lossy_mass_accuracy 1e-4 > TOPP_OpenSwathMzMLFileCacher_test_3_step1.stdout 2> TOPP_OpenSwathMzMLFileCacher_test_3_step1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathMzMLFileCacher_test_3_step1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_3_step1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_3_step1.stdout)";fi
+OpenSwathMzMLFileCacher -in OpenSwathMzMLFileCacher_3_input.tmp.sqMass -out OpenSwathMzMLFileCacher_3_output.tmp.mzML -test > TOPP_OpenSwathMzMLFileCacher_test_3_step2.stdout 2> TOPP_OpenSwathMzMLFileCacher_test_3_step2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathMzMLFileCacher_test_3_step2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_3_step2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_3_step2.stdout)";fi
+OpenSwathMzMLFileCacher -in OpenSwathMzMLFileCacher_2_input.chrom.mzML -out OpenSwathMzMLFileCacher_4_input.tmp.sqMass -test > TOPP_OpenSwathMzMLFileCacher_test_4_step1.stdout 2> TOPP_OpenSwathMzMLFileCacher_test_4_step1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathMzMLFileCacher_test_4_step1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_4_step1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_4_step1.stdout)";fi
+OpenSwathMzMLFileCacher -in OpenSwathMzMLFileCacher_4_input.tmp.sqMass -out OpenSwathMzMLFileCacher_4_output.tmp.mzML -test > TOPP_OpenSwathMzMLFileCacher_test_4_step2.stdout 2> TOPP_OpenSwathMzMLFileCacher_test_4_step2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathMzMLFileCacher_test_4_step2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_4_step2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_4_step2.stdout)";fi
+OpenSwathMzMLFileCacher -in OpenSwathMzMLFileCacher_1_input.mzML -out OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML -test -process_lowmemory > TOPP_OpenSwathMzMLFileCacher_test_5_step1.stdout 2> TOPP_OpenSwathMzMLFileCacher_test_5_step1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathMzMLFileCacher_test_5_step1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_5_step1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_5_step1.stdout)";fi
+OpenSwathMzMLFileCacher -in OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML -out OpenSwathMzMLFileCacher_1_output.tmp.mzML -convert_back -test > TOPP_OpenSwathMzMLFileCacher_test_5_step2.stdout 2> TOPP_OpenSwathMzMLFileCacher_test_5_step2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathMzMLFileCacher_test_5_step2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_5_step2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathMzMLFileCacher_test_5_step2.stdout)";fi
+OpenSwathMzMLFileCacher -in OpenSwathAnalyzer_2_swathfile.mzML -out OpenSwathAnalyzer_3_swathfile.mzML.cached.tmp -out_type mzML -test > TOPP_OpenSwathAnalyzer_test_3_prepare.stdout 2> TOPP_OpenSwathAnalyzer_test_3_prepare.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_3_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_3_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_3_prepare.stdout)";fi
+OpenSwathAnalyzer -in OpenSwathAnalyzer_1_input_chrom.mzML -tr OpenSwathAnalyzer_1_input.TraML -out MRMFeatureFinderScore_output_3.featureXML.tmp -swath_files OpenSwathAnalyzer_3_swathfile.mzML.cached.tmp -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width 40.0 -algorithm:TransitionGroupPicker:PeakPickerMRM:method legacy -test > TOPP_OpenSwathAnalyzer_test_3.stdout 2> TOPP_OpenSwathAnalyzer_test_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_3.stdout)";fi
+OpenSwathMzMLFileCacher -in OpenSwathAnalyzer_2_swathfile.mzML -out OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp -out_type mzML -test > TOPP_OpenSwathAnalyzer_test_4_prepare1.stdout 2> TOPP_OpenSwathAnalyzer_test_4_prepare1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_4_prepare1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_4_prepare1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_4_prepare1.stdout)";fi
+OpenSwathMzMLFileCacher -in OpenSwathAnalyzer_1_input_chrom.mzML -out OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp -out_type mzML -test > TOPP_OpenSwathAnalyzer_test_4_prepare2.stdout 2> TOPP_OpenSwathAnalyzer_test_4_prepare2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_4_prepare2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_4_prepare2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_4_prepare2.stdout)";fi
+OpenSwathAnalyzer -in OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp -tr OpenSwathAnalyzer_1_input.TraML -out MRMFeatureFinderScore_output_4.featureXML.tmp -swath_files OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width 40.0 -algorithm:TransitionGroupPicker:PeakPickerMRM:method legacy -test > TOPP_OpenSwathAnalyzer_test_4.stdout 2> TOPP_OpenSwathAnalyzer_test_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathAnalyzer_test_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathAnalyzer_test_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathAnalyzer_test_4.stdout)";fi
+MRMTransitionGroupPicker -in MRMTransitionGroupPicker_1_input.mzML -tr MRMTransitionGroupPicker_1_input.TraML -out MRMTransitionGroupPicker_test_1.featureXML.tmp -test -algorithm:PeakPickerMRM:remove_overlapping_peaks true -algorithm:PeakPickerMRM:method legacy -algorithm:PeakPickerMRM:peak_width 40.0 > UTILS_MRMTransitionGroupPicker_test_1.stdout 2> UTILS_MRMTransitionGroupPicker_test_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_MRMTransitionGroupPicker_test_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_MRMTransitionGroupPicker_test_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_MRMTransitionGroupPicker_test_1.stdout)";fi
+MRMTransitionGroupPicker -in MRMTransitionGroupPicker_1_input.mzML -tr MRMTransitionGroupPicker_1_input.TraML -out MRMTransitionGroupPicker_test_2.featureXML.tmp -test -algorithm:PeakPickerMRM:remove_overlapping_peaks true -algorithm:PeakPickerMRM:method legacy -algorithm:PeakPickerMRM:peak_width 40.0 -algorithm:compute_total_mi > UTILS_MRMTransitionGroupPicker_test_2.stdout 2> UTILS_MRMTransitionGroupPicker_test_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_MRMTransitionGroupPicker_test_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_MRMTransitionGroupPicker_test_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_MRMTransitionGroupPicker_test_2.stdout)";fi
+OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_1.chrom.mzML.tmp -out_features OpenSwathWorkflow_1.featureXML.tmp -out_qc OpenSwathWorkflow_1.json.tmp -test > TOPP_OpenSwathWorkflow_1.stdout 2> TOPP_OpenSwathWorkflow_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_1.stdout)";fi
+OpenSwathWorkflow -in OpenSwathWorkflow_2_input.mzXML -tr OpenSwathWorkflow_2_input.TraML -rt_norm OpenSwathWorkflow_2_input.trafoXML -out_chrom OpenSwathWorkflow_2.chrom.mzML.tmp -out_features OpenSwathWorkflow_2.featureXML.tmp -test > TOPP_OpenSwathWorkflow_2.stdout 2> TOPP_OpenSwathWorkflow_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_2.stdout)";fi
+OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_3.chrom.mzML.tmp -out_features OpenSwathWorkflow_3.featureXML.tmp -test -use_ms1_traces > TOPP_OpenSwathWorkflow_3.stdout 2> TOPP_OpenSwathWorkflow_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_3.stdout)";fi
+OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_4.chrom.mzML.tmp -out_tsv OpenSwathWorkflow_4.tsv.tmp -test -use_ms1_traces > TOPP_OpenSwathWorkflow_4.stdout 2> TOPP_OpenSwathWorkflow_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_4.stdout)";fi
+OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_5.chrom.mzML.tmp -out_features OpenSwathWorkflow_5.featureXML.tmp -test -use_ms1_traces -readOptions cache -tempDirectory "." > TOPP_OpenSwathWorkflow_5.stdout 2> TOPP_OpenSwathWorkflow_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_5.stdout)";fi
+OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_6.chrom.mzML.tmp -out_features OpenSwathWorkflow_6.featureXML.tmp -test -use_ms1_traces -readOptions cacheWorkingInMemory -tempDirectory "." > TOPP_OpenSwathWorkflow_6.stdout 2> TOPP_OpenSwathWorkflow_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_6.stdout)";fi
+OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_7.chrom.mzML.tmp -out_features OpenSwathWorkflow_7.featureXML.tmp -test -use_ms1_traces -swath_windows_file swath_windows.txt > TOPP_OpenSwathWorkflow_7.stdout 2> TOPP_OpenSwathWorkflow_7.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_7.stdout)";fi
+OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_10.chrom.mzML.tmp -out_features OpenSwathWorkflow_10.featureXML.tmp -test -use_ms1_traces -swath_windows_file swath_windows_overlap.txt -force > TOPP_OpenSwathWorkflow_10.stdout 2> TOPP_OpenSwathWorkflow_10.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_10.stdout)";fi
+OpenSwathWorkflow -in OpenSwathWorkflow_11_input.mzML -tr_irt OpenSwathWorkflow_11_input.TraML -tr OpenSwathWorkflow_11_input.TraML -mz_extraction_window 0.2 -rt_extraction_window -1 -Scoring:Scores:use_sonar_scores -sonar -out_chrom OpenSwathWorkflow_11.chrom.mzML.tmp -out_features OpenSwathWorkflow_11.featureXML.tmp -RTNormalization:outlierMethod none -mz_correction_function quadratic_regression_delta_ppm -irt_mz_extraction_window 550 -irt_mz_extraction_window_unit ppm -test > TOPP_OpenSwathWorkflow_11.stdout 2> TOPP_OpenSwathWorkflow_11.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_11 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_11.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_11.stdout)";fi
+TargetedFileConverter -test -in OpenSwathWorkflow_1_input.TraML -out OpenSwathWorkflow_13_input.pqp.tmp -out_type pqp > TOPP_OpenSwathWorkflow_13_prepare.stdout 2> TOPP_OpenSwathWorkflow_13_prepare.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_13_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_13_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_13_prepare.stdout)";fi
+OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_13_input.pqp.tmp -tr_type pqp -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_13.chrom.mzML.tmp -out_osw OpenSwathWorkflow_13.osw -test -use_ms1_traces > TOPP_OpenSwathWorkflow_13.stdout 2> TOPP_OpenSwathWorkflow_13.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_13 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_13.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_13.stdout)";fi
+TargetedFileConverter -test -in OpenSwathWorkflow_1_input.TraML -out OpenSwathWorkflow_14_input.pqp.tmp -out_type pqp > TOPP_OpenSwathWorkflow_14_prepare.stdout 2> TOPP_OpenSwathWorkflow_14_prepare.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_14_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_14_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_14_prepare.stdout)";fi
+OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_14_input.pqp.tmp -tr_type pqp -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_14.chrom.tmp.sqMass -out_osw OpenSwathWorkflow_14.osw -test -use_ms1_traces > TOPP_OpenSwathWorkflow_14.stdout 2> TOPP_OpenSwathWorkflow_14.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_14 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_14.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_14.stdout)";fi
+OpenSwathMzMLFileCacher -in OpenSwathWorkflow_14.chrom.tmp.sqMass -out OpenSwathWorkflow_14.chrom.tmp.mzML -test -lossy_compression false -lossy_mass_accuracy 1e-4 -full_meta false > TOPP_OpenSwathWorkflow_14_step2.stdout 2> TOPP_OpenSwathWorkflow_14_step2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_14_step2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_14_step2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_14_step2.stdout)";fi
+OpenSwathWorkflow -in OpenSwathWorkflow_15_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_15.chrom.mzML.tmp -out_features OpenSwathWorkflow_15.featureXML.tmp -test -use_ms1_traces -Scoring:TransitionGroupPicker:compute_peak_quality false -Scoring:TransitionGroupPicker:use_precursors -ms1_isotopes 2 > TOPP_OpenSwathWorkflow_15.stdout 2> TOPP_OpenSwathWorkflow_15.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_15 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_15.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_15.stdout)";fi
+OpenSwathMzMLFileCacher -in OpenSwathWorkflow_1_input.mzML -out OpenSwathWorkflow_16_input.sqMass -test -lossy_compression true -lossy_mass_accuracy 1e-4 -full_meta true > TOPP_OpenSwathWorkflow_16_prepare.stdout 2> TOPP_OpenSwathWorkflow_16_prepare.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_16_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_16_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_16_prepare.stdout)";fi
+OpenSwathWorkflow -in OpenSwathWorkflow_16_input.sqMass -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_chrom OpenSwathWorkflow_16.chrom.mzML.tmp -out_features OpenSwathWorkflow_16.featureXML.tmp -test -use_ms1_traces -readOptions workingInMemory -ms1_isotopes 2 > TOPP_OpenSwathWorkflow_16.stdout 2> TOPP_OpenSwathWorkflow_16.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_16 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_16.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_16.stdout)";fi
+OpenSwathWorkflow -in OpenSwathWorkflow_17_input.mzML -tr OpenSwathWorkflow_17_input.tsv -out_chrom OpenSwathWorkflow_17.chrom.mzML.tmp -out_features OpenSwathWorkflow_17.featureXML.tmp -test -use_ms1_traces -readOptions workingInMemory -ion_mobility_window 0.05 -use_ms1_ion_mobility "false" -Scoring:Scores:use_ion_mobility_scores > TOPP_OpenSwathWorkflow_17.stdout 2> TOPP_OpenSwathWorkflow_17.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_17 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_17.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_17.stdout)";fi
+OpenSwathWorkflow -in OpenSwathWorkflow_17_input.mzML -tr OpenSwathWorkflow_17_input.tsv -out_chrom OpenSwathWorkflow_17.chrom.mzML.tmp -out_features OpenSwathWorkflow_17.featureXML.tmp -test -use_ms1_traces -readOptions cache -ion_mobility_window 0.05 -use_ms1_ion_mobility "false" -Scoring:Scores:use_ion_mobility_scores > TOPP_OpenSwathWorkflow_17_cache.stdout 2> TOPP_OpenSwathWorkflow_17_cache.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_17_cache failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_17_cache.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_17_cache.stdout)";fi
+TargetedFileConverter -test -in OpenSwathWorkflow_17_input.tsv -out OpenSwathWorkflow_17_input.pqp.tmp -out_type pqp > TOPP_OpenSwathWorkflow_17_b_prepare.stdout 2> TOPP_OpenSwathWorkflow_17_b_prepare.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_17_b_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_17_b_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_17_b_prepare.stdout)";fi
+OpenSwathWorkflow -in OpenSwathWorkflow_17_input.mzML -tr_type pqp -tr OpenSwathWorkflow_17_input.pqp.tmp -out_chrom OpenSwathWorkflow_17_b.chrom.mzML.tmp -out_features OpenSwathWorkflow_17_b.featureXML.tmp -test -use_ms1_traces -readOptions workingInMemory -ion_mobility_window 0.05 -use_ms1_ion_mobility "false" > TOPP_OpenSwathWorkflow_17_b.stdout 2> TOPP_OpenSwathWorkflow_17_b.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_17_b failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_17_b.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_17_b.stdout)";fi
+OpenSwathFileSplitter -in OpenSwathWorkflow_1_input.mzML -outputDirectory "" -out_qc OpenSwathFileSplitter_1.json.tmp -test > TOPP_OpenSwathFileSplitter_1.stdout 2> TOPP_OpenSwathFileSplitter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathFileSplitter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathFileSplitter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathFileSplitter_1.stdout)";fi
+OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_features OpenSwathWorkflow_18.featureXML.tmp -test -use_ms1_traces -Scoring:Scores:use_ms1_mi > TOPP_OpenSwathWorkflow_18.stdout 2> TOPP_OpenSwathWorkflow_18.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_18 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_18.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_18.stdout)";fi
+OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_features OpenSwathWorkflow_19.featureXML.tmp -test -use_ms1_traces -Scoring:Scores:use_mi_score > TOPP_OpenSwathWorkflow_19.stdout 2> TOPP_OpenSwathWorkflow_19.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_19 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_19.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_19.stdout)";fi
+OpenSwathWorkflow -in OpenSwathWorkflow_1_input.mzML -tr OpenSwathWorkflow_1_input.TraML -rt_norm OpenSwathWorkflow_1_input.trafoXML -out_features OpenSwathWorkflow_20.featureXML.tmp -test -use_ms1_traces -Scoring:Scores:use_mi_score -Scoring:Scores:use_total_mi_score > TOPP_OpenSwathWorkflow_20.stdout 2> TOPP_OpenSwathWorkflow_20.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_20 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_20.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_20.stdout)";fi
+OpenSwathWorkflow -in OpenSwathWorkflow_21_input.mzML -tr OpenSwathWorkflow_21_input.tsv -tr_irt OpenSwathWorkflow_21_input.irt.TraML -out_features OpenSwathWorkflow_21.featureXML.tmp -Debugging:irt_trafo OpenSwathWorkflow_21.trafoXML.tmp -out_chrom OpenSwathWorkflow_21.mzML.tmp -test -use_ms1_traces -Scoring:Scores:use_mi_score -Scoring:Scores:use_total_mi_score > TOPP_OpenSwathWorkflow_21.stdout 2> TOPP_OpenSwathWorkflow_21.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_21 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_21.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_21.stdout)";fi
+OpenSwathWorkflow -in OpenSwathWorkflow_22_input.mzML -tr OpenSwathWorkflow_22_input.tsv -out_chrom OpenSwathWorkflow_22.chrom.mzML.tmp -out_features OpenSwathWorkflow_22.featureXML.tmp -test -use_ms1_traces -readOptions workingInMemory -matching_window_only "true" -ms1_isotopes 3 > TOPP_OpenSwathWorkflow_22.stdout 2> TOPP_OpenSwathWorkflow_22.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenSwathWorkflow_22 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenSwathWorkflow_22.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenSwathWorkflow_22.stdout)";fi
+NoiseFilterGaussian -test -ini NoiseFilterGaussian_1_parameters.ini -in NoiseFilterGaussian_1_input.mzML -out NoiseFilterGaussian_1.tmp > TOPP_NoiseFilterGaussian_1.stdout 2> TOPP_NoiseFilterGaussian_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_NoiseFilterGaussian_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_NoiseFilterGaussian_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_NoiseFilterGaussian_1.stdout)";fi
+NoiseFilterGaussian -test -ini NoiseFilterGaussian_2_parameters.ini -in NoiseFilterGaussian_2_input.chrom.mzML -out NoiseFilterGaussian_2.tmp > TOPP_NoiseFilterGaussian_2.stdout 2> TOPP_NoiseFilterGaussian_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_NoiseFilterGaussian_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_NoiseFilterGaussian_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_NoiseFilterGaussian_2.stdout)";fi
+NoiseFilterGaussian -test -ini NoiseFilterGaussian_1_parameters.ini -in NoiseFilterGaussian_1_input.mzML -out NoiseFilterGaussian_3.tmp -processOption lowmemory > TOPP_NoiseFilterGaussian_3.stdout 2> TOPP_NoiseFilterGaussian_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_NoiseFilterGaussian_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_NoiseFilterGaussian_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_NoiseFilterGaussian_3.stdout)";fi
+NoiseFilterGaussian -test -ini NoiseFilterGaussian_2_parameters.ini -in NoiseFilterGaussian_2_input.chrom.mzML -out NoiseFilterGaussian_4.tmp -processOption lowmemory > TOPP_NoiseFilterGaussian_4.stdout 2> TOPP_NoiseFilterGaussian_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_NoiseFilterGaussian_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_NoiseFilterGaussian_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_NoiseFilterGaussian_4.stdout)";fi
+NoiseFilterSGolay -test -ini NoiseFilterSGolay_1_parameters.ini -in NoiseFilterSGolay_1_input.mzML -out NoiseFilterSGolay_1.tmp > TOPP_NoiseFilterSGolay_1.stdout 2> TOPP_NoiseFilterSGolay_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_NoiseFilterSGolay_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_NoiseFilterSGolay_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_NoiseFilterSGolay_1.stdout)";fi
+NoiseFilterSGolay -test -ini NoiseFilterSGolay_2_parameters.ini -in NoiseFilterSGolay_2_input.chrom.mzML -out NoiseFilterSGolay_2.tmp > TOPP_NoiseFilterSGolay_2.stdout 2> TOPP_NoiseFilterSGolay_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_NoiseFilterSGolay_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_NoiseFilterSGolay_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_NoiseFilterSGolay_2.stdout)";fi
+NoiseFilterSGolay -test -ini NoiseFilterSGolay_1_parameters.ini -in NoiseFilterSGolay_1_input.mzML -out NoiseFilterSGolay_3.tmp -processOption lowmemory > TOPP_NoiseFilterSGolay_3.stdout 2> TOPP_NoiseFilterSGolay_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_NoiseFilterSGolay_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_NoiseFilterSGolay_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_NoiseFilterSGolay_3.stdout)";fi
+NoiseFilterSGolay -test -ini NoiseFilterSGolay_2_parameters.ini -in NoiseFilterSGolay_2_input.chrom.mzML -out NoiseFilterSGolay_4.tmp -processOption lowmemory > TOPP_NoiseFilterSGolay_4.stdout 2> TOPP_NoiseFilterSGolay_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_NoiseFilterSGolay_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_NoiseFilterSGolay_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_NoiseFilterSGolay_4.stdout)";fi
+PeakPickerWavelet -test -ini PeakPickerWavelet_parameters.ini -in PeakPickerWavelet_input.mzML -out PeakPickerWavelet_1.tmp > TOPP_PeakPickerWavelet_1.stdout 2> TOPP_PeakPickerWavelet_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeakPickerWavelet_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeakPickerWavelet_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeakPickerWavelet_1.stdout)";fi
+PeakPickerWavelet -test -ini PeakPickerWavelet_deconv_parameters.ini -in PeakPickerWavelet_deconv_input.mzML -out PeakPickerWavelet_2.tmp > TOPP_PeakPickerWavelet_2.stdout 2> TOPP_PeakPickerWavelet_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeakPickerWavelet_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeakPickerWavelet_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeakPickerWavelet_2.stdout)";fi
+PeakPickerWavelet -test -ini PeakPickerWavelet_parameters.ini -in PeakPickerWavelet_input.mzML -out PeakPickerWavelet_4.tmp -threads 2 > TOPP_PeakPickerWavelet_4.stdout 2> TOPP_PeakPickerWavelet_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeakPickerWavelet_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeakPickerWavelet_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeakPickerWavelet_4.stdout)";fi
+PeakPickerWavelet -test -ini PeakPickerWavelet_parameters_noMetaData.ini -in PeakPickerWavelet_input.mzML -out PeakPickerWavelet_5.tmp -threads 2 > TOPP_PeakPickerWavelet_5.stdout 2> TOPP_PeakPickerWavelet_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeakPickerWavelet_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeakPickerWavelet_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeakPickerWavelet_5.stdout)";fi
+PeakPickerHiRes -test -ini PeakPickerHiRes_parameters.ini -in PeakPickerHiRes_input.mzML -out PeakPickerHiRes_1.tmp > TOPP_PeakPickerHiRes_1.stdout 2> TOPP_PeakPickerHiRes_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeakPickerHiRes_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeakPickerHiRes_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeakPickerHiRes_1.stdout)";fi
+PeakPickerHiRes -test -ini PeakPickerHiRes_parameters.ini -in PeakPickerHiRes_2_input.mzML -out PeakPickerHiRes_2.tmp > TOPP_PeakPickerHiRes_2.stdout 2> TOPP_PeakPickerHiRes_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeakPickerHiRes_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeakPickerHiRes_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeakPickerHiRes_2.stdout)";fi
+PeakPickerHiRes -test -ini PeakPickerHiRes_parameters.ini -in PeakPickerHiRes_input.mzML -out PeakPickerHiRes_3.tmp -processOption lowmemory > TOPP_PeakPickerHiRes_3.stdout 2> TOPP_PeakPickerHiRes_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeakPickerHiRes_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeakPickerHiRes_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeakPickerHiRes_3.stdout)";fi
+PeakPickerHiRes -test -ini PeakPickerHiRes_parameters.ini -in PeakPickerHiRes_2_input.mzML -out PeakPickerHiRes_4.tmp -processOption lowmemory > TOPP_PeakPickerHiRes_4.stdout 2> TOPP_PeakPickerHiRes_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeakPickerHiRes_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeakPickerHiRes_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeakPickerHiRes_4.stdout)";fi
+PeakPickerHiRes -test -in PeakPickerHiRes_5_input.mzML -out PeakPickerHiRes_5.tmp > TOPP_PeakPickerHiRes_5.stdout 2> TOPP_PeakPickerHiRes_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeakPickerHiRes_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeakPickerHiRes_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeakPickerHiRes_5.stdout)";fi
+PeakPickerIterative -in PeakPickerIterative_1_input.mzML -ini PeakPickerIterative_1.ini -out PeakPickerIterative.mzML.tmp -test > UTILS_PeakPickerIterative_1.stdout 2> UTILS_PeakPickerIterative_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_PeakPickerIterative_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_PeakPickerIterative_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_PeakPickerIterative_1.stdout)";fi
+PeakPickerIterative -in PeakPickerIterative_2_input.mzML -ini PeakPickerIterative_2.ini -out PeakPickerIterative_2.mzML.tmp -test > UTILS_PeakPickerIterative_2.stdout 2> UTILS_PeakPickerIterative_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_PeakPickerIterative_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_PeakPickerIterative_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_PeakPickerIterative_2.stdout)";fi
+LowMemPeakPickerHiRes -test -ini LowMemPeakPickerHiRes_parameters.ini -in PeakPickerHiRes_input.mzML -out LowMemPeakPickerHiRes_1.tmp > TOPP_LowMemPeakPickerHiRes_1.stdout 2> TOPP_LowMemPeakPickerHiRes_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_LowMemPeakPickerHiRes_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_LowMemPeakPickerHiRes_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_LowMemPeakPickerHiRes_1.stdout)";fi
+LowMemPeakPickerHiResRandomAccess -test -ini LowMemPeakPickerHiRes_RandomAccess_parameters.ini -in PeakPickerHiRes_RandomAccess_input.mzML -out LowMemPeakPickerHiRes_RandomAccess_1.tmp > TOPP_LowMemPeakPickerHiResRandomAccess_1.stdout 2> TOPP_LowMemPeakPickerHiResRandomAccess_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_LowMemPeakPickerHiResRandomAccess_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_LowMemPeakPickerHiResRandomAccess_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_LowMemPeakPickerHiResRandomAccess_1.stdout)";fi
+ProteinInference -test -in ProteinInference_1_input.idXML -out ProteinInference_1_output.tmp -Algorithm:use_shared_peptides false -merge_runs all -Merging:annotate_origin false > TOPP_ProteinInference_1.stdout 2> TOPP_ProteinInference_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinInference_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinInference_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinInference_1.stdout)";fi
+Resampler -test -in Resampler_1_input.mzML -out Resampler.mzML -sampling_rate 0.3 > TOPP_Resampler_1.stdout 2> TOPP_Resampler_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_Resampler_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_Resampler_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_Resampler_1.stdout)";fi
+RNPxlSearch -test -in RNPxlSearch_1_input.mzML -database RNPxlSearch_1_input.fasta -out RNPxlSearch_1_output.tmp -ini RNPxlSearch_1_parameters.ini > TOPP_RNPxlSearch_1.stdout 2> TOPP_RNPxlSearch_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RNPxlSearch_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RNPxlSearch_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RNPxlSearch_1.stdout)";fi
+RNPxlSearch -test -in RNPxlSearch_1_input.mzML -database RNPxlSearch_1_input.fasta -out RNPxlSearch_2_output.tmp -RNPxl:decoys -ini RNPxlSearch_1_parameters.ini > TOPP_RNPxlSearch_2.stdout 2> TOPP_RNPxlSearch_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RNPxlSearch_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RNPxlSearch_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RNPxlSearch_2.stdout)";fi
+RNPxlSearch -test -in RNPxlSearch_1_input.mzML -database RNPxlSearch_1_input.fasta -out RNPxlSearch_3_output.tmp -report:top_hits 3 -out_tsv RNPxlSearch_3_output2.tmp -precursor:mass_tolerance 10 -RNPxl:scoring fast > TOPP_RNPxlSearch_3.stdout 2> TOPP_RNPxlSearch_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RNPxlSearch_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RNPxlSearch_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RNPxlSearch_3.stdout)";fi
+RNPxlSearch -test -in RNPxlSearch_1_input.mzML -RNPxl:decoys -database RNPxlSearch_1_input.fasta -out RNPxlSearch_4_output.tmp -report:top_hits 2 -out_tsv RNPxlSearch_4_output2.tmp -precursor:mass_tolerance 10 -RNPxl:scoring fast > TOPP_RNPxlSearch_4.stdout 2> TOPP_RNPxlSearch_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RNPxlSearch_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RNPxlSearch_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RNPxlSearch_4.stdout)";fi
+RTModel -test -in RTModel_1_input.idXML -out RTModel_1_output.tmp -ini RTModel_1_parameters.ini > TOPP_RTModel_1.stdout 2> TOPP_RTModel_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RTModel_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RTModel_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RTModel_1.stdout)";fi
+RTModel -test -in_positive RTModel_2_input_positive.idXML -in_negative RTModel_2_input_negative.idXML -out RTModel_2_output.tmp -ini RTModel_2_parameters.ini > TOPP_RTModel_2.stdout 2> TOPP_RTModel_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RTModel_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RTModel_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RTModel_2.stdout)";fi
+RTModel -test -in RTModel_3_input.idXML -out RTModel_3_output.tmp -ini RTModel_3_parameters.ini > TOPP_RTModel_3.stdout 2> TOPP_RTModel_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RTModel_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RTModel_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RTModel_3.stdout)";fi
+RTModel -test -in RTModel_4_input.txt -out RTModel_4_output.tmp -ini RTModel_4_parameters.ini > TOPP_RTModel_4.stdout 2> TOPP_RTModel_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RTModel_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RTModel_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RTModel_4.stdout)";fi
+PTModel -test -in_positive PTModel_1_input_positive.idXML -in_negative PTModel_1_input_negative.idXML -out PTModel_1_output.tmp -ini PTModel_1_parameters.ini > TOPP_PTModel_1.stdout 2> TOPP_PTModel_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PTModel_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PTModel_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PTModel_1.stdout)";fi
+PTPredict -test -in PTPredict_1_input.idXML -out PTPredict_1_output.tmp -svm_model PTPredict_1_input.model > TOPP_PTPredict_1.stdout 2> TOPP_PTPredict_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PTPredict_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PTPredict_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PTPredict_1.stdout)";fi
+RTPredict -test -in_id RTPredict_1_input.idXML -out_id:file RTPredict_1_output.tmp -total_gradient_time 3000 -svm_model RTPredict_1_input.model > TOPP_RTPredict_1.stdout 2> TOPP_RTPredict_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RTPredict_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RTPredict_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RTPredict_1.stdout)";fi
+RTPredict -test -in_id RTPredict_2_input.idXML -out_id:positive RTPredict_2_output_positive.tmp -out_id:negative RTPredict_2_output_negative.tmp -svm_model RTPredict_2_input.model -in_oligo_params RTPredict_2_input.model_additional_parameters.paramXML -in_oligo_trainset RTPredict_2_input.model_samples > TOPP_RTPredict_2.stdout 2> TOPP_RTPredict_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RTPredict_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RTPredict_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RTPredict_2.stdout)";fi
+RTPredict -test -in_id RTPredict_3_input.idXML -out_id:file RTPredict_3_output.tmp -total_gradient_time 1 -svm_model RTPredict_3_input.model -in_oligo_params RTPredict_3_input.model_additional_parameters.paramXML -in_oligo_trainset RTPredict_3_input.model_samples > TOPP_RTPredict_3.stdout 2> TOPP_RTPredict_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RTPredict_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RTPredict_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RTPredict_3.stdout)";fi
+RTPredict -test -in_text RTPredict_4_input.txt -out_text:file RTPredict_4_output.tmp -total_gradient_time 1 -svm_model RTPredict_4_input.model -in_oligo_params RTPredict_4_input.model_additional_parameters.paramXML -in_oligo_trainset RTPredict_4_input.model_samples > TOPP_RTPredict_4.stdout 2> TOPP_RTPredict_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RTPredict_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RTPredict_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RTPredict_4.stdout)";fi
+RTPredict -test -in_id RTPredict_5_input.idXML -out_text:file RTPredict_5_output.tmp -total_gradient_time 1 -svm_model RTPredict_5_input.model -in_oligo_params RTPredict_5_input.model_additional_parameters.paramXML -in_oligo_trainset RTPredict_5_input.model_samples > TOPP_RTPredict_5.stdout 2> TOPP_RTPredict_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_RTPredict_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_RTPredict_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_RTPredict_5.stdout)";fi
+InspectAdapter -test -ini InspectAdapter_1_parameters.ini -trie_dbs Inspect_FASTAFile_test2.trie -in Inspect.mzXML -dbs Inspect_FASTAFile_test.fasta -inspect_in -out InspectAdapter_2_output.tmp > TOPP_InspectAdapter_1.stdout 2> TOPP_InspectAdapter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InspectAdapter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_InspectAdapter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InspectAdapter_1.stdout)";fi
+InspectAdapter -test -ini InspectAdapter_1_parameters.ini -trie_dbs Inspect_FASTAFile_test2.trie -in Inspect.mzData -dbs Inspect_FASTAFile_test.fasta -inspect_in -out InspectAdapter_3_output.tmp > TOPP_InspectAdapter_2.stdout 2> TOPP_InspectAdapter_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InspectAdapter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_InspectAdapter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InspectAdapter_2.stdout)";fi
+SeedListGenerator -test -in PepXMLFile_test.mzML -out SeedListGenerator_1_output.tmp > TOPP_SeedListGenerator_1.stdout 2> TOPP_SeedListGenerator_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SeedListGenerator_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SeedListGenerator_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SeedListGenerator_1.stdout)";fi
+SeedListGenerator -test -in IDMapper_1_output.featureXML -out SeedListGenerator_2_output.tmp > TOPP_SeedListGenerator_2.stdout 2> TOPP_SeedListGenerator_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SeedListGenerator_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SeedListGenerator_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SeedListGenerator_2.stdout)";fi
+SeedListGenerator -test -in ConsensusXMLFile_1.consensusXML -out SeedListGenerator_3_output1.tmp SeedListGenerator_3_output2.tmp > TOPP_SeedListGenerator_3.stdout 2> TOPP_SeedListGenerator_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SeedListGenerator_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SeedListGenerator_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SeedListGenerator_3.stdout)";fi
+SpectraFilterSqrtMower -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterSqrtMower.tmp > TOPP_SpectraFilterSqrtMower_1.stdout 2> TOPP_SpectraFilterSqrtMower_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SpectraFilterSqrtMower_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SpectraFilterSqrtMower_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SpectraFilterSqrtMower_1.stdout)";fi
+SpectraFilterWindowMower -test -in SpectraFilterWindowMower_1_input.mzML -out SpectraFilterWindowMower_1.tmp > TOPP_SpectraFilterWindowMower_1.stdout 2> TOPP_SpectraFilterWindowMower_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SpectraFilterWindowMower_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SpectraFilterWindowMower_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SpectraFilterWindowMower_1.stdout)";fi
+SpectraFilterWindowMower -test -in SpectraFilterWindowMower_2_input.mzML -out SpectraFilterWindowMower_2.tmp -ini SpectraFilterWindowMower_2_parameters.ini > TOPP_SpectraFilterWindowMower_2.stdout 2> TOPP_SpectraFilterWindowMower_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SpectraFilterWindowMower_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SpectraFilterWindowMower_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SpectraFilterWindowMower_2.stdout)";fi
+InternalCalibration -test -in InternalCalibration_1_BSA1.mzML -cal:id_in InternalCalibration_1_BSA1_OMSSA.idXML -out InternalCalibration_1_BSA1_out.mzML.tmp -cal:model_type linear -RANSAC:enabled -RANSAC:iter 500 -RANSAC:threshold 1 -RT_chunking -1 -quality_control:models InternalCalibration_1_models.csv.tmp -quality_control:residuals InternalCalibration_1_residuals.csv.tmp -ms_level 1 > TOPP_InternalCalibration_1.stdout 2> TOPP_InternalCalibration_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InternalCalibration_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_InternalCalibration_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InternalCalibration_1.stdout)";fi
+InternalCalibration -test -in InternalCalibration_2_lockmass.mzML.gz -cal:lock_in InternalCalibration_2_lock.csv -out InternalCalibration_2_lockmass.mzML.tmp -cal:lock_require_mono -cal:model_type linear -RT_chunking 60 -quality_control:models InternalCalibration_2_models.csv.tmp -quality_control:residuals InternalCalibration_2_residuals.csv.tmp > TOPP_InternalCalibration_2.stdout 2> TOPP_InternalCalibration_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InternalCalibration_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_InternalCalibration_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InternalCalibration_2.stdout)";fi
+FileConverter -test -in InternalCalibration_2_lockmass.mzML.tmp -no_progress -out InternalCalibration_2_out_lockmass.dta2d.tmp -out_type dta2d > TOPP_InternalCalibration_2_convert.stdout 2> TOPP_InternalCalibration_2_convert.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InternalCalibration_2_convert failed'; >&2 echo -e "stderr:\n$(cat TOPP_InternalCalibration_2_convert.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InternalCalibration_2_convert.stdout)";fi
+ExternalCalibration -test -in ExternalCalibration_1_input.mzML -out ExternalCalibration_1_MS1_out.mzML.tmp -offset -5.5 -slope 0.0001 -ms_level 1 > TOPP_ExternalCalibration_1_MS1.stdout 2> TOPP_ExternalCalibration_1_MS1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ExternalCalibration_1_MS1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ExternalCalibration_1_MS1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ExternalCalibration_1_MS1.stdout)";fi
+ExternalCalibration -test -in ExternalCalibration_1_input.mzML -out ExternalCalibration_2_MS2_out.mzML.tmp -offset -5.5 -slope 0.0001 -ms_level 2 > TOPP_ExternalCalibration_2_MS2.stdout 2> TOPP_ExternalCalibration_2_MS2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ExternalCalibration_2_MS2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ExternalCalibration_2_MS2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ExternalCalibration_2_MS2.stdout)";fi
+TOFCalibration -test -in TOFCalibration_1_input.mzML -out TOFCalibration.tmp -ref_masses TOFCalibration_ref_masses.txt -ini TOFCalibration_parameters.ini -tof_const TOFCalibration_const.csv -ext_calibrants TOFCalibration_1_calibrants.mzML > TOPP_TOFCalibration_1.stdout 2> TOPP_TOFCalibration_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TOFCalibration_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TOFCalibration_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TOFCalibration_1.stdout)";fi
+TOFCalibration -test -in TOFCalibration_2_input.mzML -out TOFCalibration_2.tmp -ref_masses TOFCalibration_ref_masses.txt -ini TOFCalibration_parameters.ini -tof_const TOFCalibration_const.csv -ext_calibrants TOFCalibration_2_calibrants.mzML -peak_data > TOPP_TOFCalibration_2.stdout 2> TOPP_TOFCalibration_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TOFCalibration_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TOFCalibration_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TOFCalibration_2.stdout)";fi
+TextExporter -test -in TextExporter_1_input.featureXML -no_progress -out TextExporter_1_output.tmp > TOPP_TextExporter_1.stdout 2> TOPP_TextExporter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TextExporter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TextExporter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TextExporter_1.stdout)";fi
+TextExporter -test -in TextExporter_2_input.consensusXML -ini TextExporter_2_parameters.ini > TOPP_TextExporter_2.stdout 2> TOPP_TextExporter_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TextExporter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TextExporter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TextExporter_2.stdout)";fi
+TextExporter -test -in TextExporter_3_input.idXML -no_progress -out TextExporter_3_output.tmp > TOPP_TextExporter_3.stdout 2> TOPP_TextExporter_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TextExporter_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TextExporter_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TextExporter_3.stdout)";fi
+TextExporter -test -in TextExporter_3_input.idXML -no_progress -out TextExporter_4_output.tmp -id:proteins_only > TOPP_TextExporter_4.stdout 2> TOPP_TextExporter_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TextExporter_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TextExporter_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TextExporter_4.stdout)";fi
+TextExporter -test -in TextExporter_5_input.idXML -no_progress -out TextExporter_5_output.tmp -id:peptides_only -id:first_dim_rt > TOPP_TextExporter_5.stdout 2> TOPP_TextExporter_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TextExporter_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TextExporter_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TextExporter_5.stdout)";fi
+TextExporter -test -in TextExporter_6_input.featureXML -no_progress -out TextExporter_6_output.tmp -no_ids > TOPP_TextExporter_6.stdout 2> TOPP_TextExporter_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TextExporter_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TextExporter_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TextExporter_6.stdout)";fi
+TextExporter -test -in TextExporter_7_input.consensusXML -ini TextExporter_7_parameters.ini > TOPP_TextExporter_7.stdout 2> TOPP_TextExporter_7.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TextExporter_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TextExporter_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TextExporter_7.stdout)";fi
+TextExporter -test -in TextExporter_1_input.featureXML -no_ids -no_progress -out TextExporter_8_output.tmp > TOPP_TextExporter_8.stdout 2> TOPP_TextExporter_8.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TextExporter_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TextExporter_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TextExporter_8.stdout)";fi
+TextExporter -test -in TextExporter_9_input.idXML -no_progress -out TextExporter_9_output.tmp -id:add_metavalues 0 -id:add_hit_metavalues 0 > TOPP_TextExporter_9.stdout 2> TOPP_TextExporter_9.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_TextExporter_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_TextExporter_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_TextExporter_9.stdout)";fi
+FeatureLinkerLabeled -test -ini FeatureLinkerLabeled_1_parameters.ini -in FeatureLinkerLabeled_1_input.featureXML -out FeatureLinkerLabeled_1_output.tmp > TOPP_FeatureLinkerLabeled_1.stdout 2> TOPP_FeatureLinkerLabeled_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerLabeled_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerLabeled_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerLabeled_1.stdout)";fi
+FeatureLinkerLabeled -test -ini FeatureLinkerLabeled_2_parameters.ini -in FeatureLinkerLabeled_2_input.featureXML -out FeatureLinkerLabeled_2_output.tmp > TOPP_FeatureLinkerLabeled_2.stdout 2> TOPP_FeatureLinkerLabeled_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerLabeled_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerLabeled_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerLabeled_2.stdout)";fi
+FeatureLinkerUnlabeled -test -ini FeatureLinkerUnlabeled_1_parameters.ini -in FeatureLinkerUnlabeled_1_input1.featureXML FeatureLinkerUnlabeled_1_input2.featureXML FeatureLinkerUnlabeled_1_input3.featureXML -out FeatureLinkerUnlabeled_1_output.tmp > TOPP_FeatureLinkerUnlabeled_1.stdout 2> TOPP_FeatureLinkerUnlabeled_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeled_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeled_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeled_1.stdout)";fi
+FeatureLinkerUnlabeled -test -ini FeatureLinkerUnlabeled_2_parameters.ini -in FeatureLinkerUnlabeled_2_input1.featureXML FeatureLinkerUnlabeled_2_input2.featureXML FeatureLinkerUnlabeled_2_input3.featureXML -out FeatureLinkerUnlabeled_2_output.tmp > TOPP_FeatureLinkerUnlabeled_2.stdout 2> TOPP_FeatureLinkerUnlabeled_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeled_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeled_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeled_2.stdout)";fi
+FeatureLinkerUnlabeled -test -ini FeatureLinkerUnlabeled_3_parameters.ini -in FeatureLinkerUnlabeled_3_input1.featureXML FeatureLinkerUnlabeled_3_input2.featureXML -out FeatureLinkerUnlabeled_3_output.tmp > TOPP_FeatureLinkerUnlabeled_3.stdout 2> TOPP_FeatureLinkerUnlabeled_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeled_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeled_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeled_3.stdout)";fi
+FeatureLinkerUnlabeled -test -ini FeatureLinkerUnlabeled_4_parameters.ini -in FeatureLinkerUnlabeled_1_input1.featureXML FeatureLinkerUnlabeled_1_input2.featureXML FeatureLinkerUnlabeled_1_input3.featureXML -out FeatureLinkerUnlabeled_4_output.tmp > TOPP_FeatureLinkerUnlabeled_4.stdout 2> TOPP_FeatureLinkerUnlabeled_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeled_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeled_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeled_4.stdout)";fi
+FeatureLinkerUnlabeledQT -test -ini FeatureLinkerUnlabeledQT_1_parameters.ini -in FeatureLinkerUnlabeled_1_input1.featureXML FeatureLinkerUnlabeled_1_input2.featureXML FeatureLinkerUnlabeled_1_input3.featureXML -out FeatureLinkerUnlabeledQT_1_output.tmp > TOPP_FeatureLinkerUnlabeledQT_1.stdout 2> TOPP_FeatureLinkerUnlabeledQT_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledQT_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledQT_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledQT_1.stdout)";fi
+FeatureLinkerUnlabeledQT -test -ini FeatureLinkerUnlabeledQT_2_parameters.ini -in FeatureLinkerUnlabeledQT_1_output.consensusXML FeatureLinkerUnlabeledQT_1_output.consensusXML -out FeatureLinkerUnlabeledQT_2_output.tmp > TOPP_FeatureLinkerUnlabeledQT_2.stdout 2> TOPP_FeatureLinkerUnlabeledQT_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledQT_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledQT_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledQT_2.stdout)";fi
+FeatureLinkerUnlabeledQT -test -ini FeatureLinkerUnlabeledQT_3_parameters.ini -in FeatureLinkerUnlabeledQT_3_input1.featureXML FeatureLinkerUnlabeledQT_3_input2.featureXML -out FeatureLinkerUnlabeledQT_3_output.tmp > TOPP_FeatureLinkerUnlabeledQT_3.stdout 2> TOPP_FeatureLinkerUnlabeledQT_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledQT_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledQT_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledQT_3.stdout)";fi
+FeatureLinkerUnlabeledQT -test -ini FeatureLinkerUnlabeledQT_1_parameters.ini -in FeatureLinkerUnlabeled_1_input1.featureXML FeatureLinkerUnlabeled_1_input2.featureXML FeatureLinkerUnlabeled_1_input3.featureXML -out FeatureLinkerUnlabeledQT_4_output.tmp -algorithm:use_identifications > TOPP_FeatureLinkerUnlabeledQT_4.stdout 2> TOPP_FeatureLinkerUnlabeledQT_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledQT_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledQT_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledQT_4.stdout)";fi
+FeatureLinkerUnlabeledQT -test -ini FeatureLinkerUnlabeledQT_1_parameters.ini -in FeatureLinkerUnlabeledQT_5_input1.featureXML FeatureLinkerUnlabeledQT_5_input2.featureXML FeatureLinkerUnlabeledQT_5_input3.featureXML -out FeatureLinkerUnlabeledQT_5_output.tmp -algorithm:distance_RT:max_difference 200 > TOPP_FeatureLinkerUnlabeledQT_5.stdout 2> TOPP_FeatureLinkerUnlabeledQT_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledQT_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledQT_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledQT_5.stdout)";fi
+FeatureLinkerUnlabeledQT -test -in FeatureLinkerUnlabeledQT_5_input1.featureXML FeatureLinkerUnlabeledQT_5_input2.featureXML FeatureLinkerUnlabeledQT_5_input3.featureXML -out FeatureLinkerUnlabeledQT_6_output.tmp -algorithm:use_identifications -algorithm:distance_RT:max_difference 200 > TOPP_FeatureLinkerUnlabeledQT_6.stdout 2> TOPP_FeatureLinkerUnlabeledQT_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledQT_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledQT_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledQT_6.stdout)";fi
+FeatureLinkerUnlabeledKD -test -ini FeatureLinkerUnlabeledKD_1_parameters.ini -in FeatureLinkerUnlabeled_1_input1.featureXML FeatureLinkerUnlabeled_1_input2.featureXML FeatureLinkerUnlabeled_1_input3.featureXML -out FeatureLinkerUnlabeledKD_1_output.tmp > TOPP_FeatureLinkerUnlabeledKD_1.stdout 2> TOPP_FeatureLinkerUnlabeledKD_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledKD_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledKD_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledKD_1.stdout)";fi
+FeatureLinkerUnlabeledKD -test -ini FeatureLinkerUnlabeledKD_2_parameters.ini -in FeatureLinkerUnlabeledKD_1_output.consensusXML FeatureLinkerUnlabeledKD_1_output.consensusXML -out FeatureLinkerUnlabeledKD_2_output.tmp > TOPP_FeatureLinkerUnlabeledKD_2.stdout 2> TOPP_FeatureLinkerUnlabeledKD_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledKD_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledKD_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledKD_2.stdout)";fi
+FeatureLinkerUnlabeledKD -test -ini FeatureLinkerUnlabeledKD_3_parameters.ini -in FeatureLinkerUnlabeledQT_3_input1.featureXML FeatureLinkerUnlabeledQT_3_input2.featureXML -out FeatureLinkerUnlabeledKD_3_output.tmp > TOPP_FeatureLinkerUnlabeledKD_3.stdout 2> TOPP_FeatureLinkerUnlabeledKD_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledKD_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledKD_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledKD_3.stdout)";fi
+FeatureLinkerUnlabeledKD -test -ini FeatureLinkerUnlabeledKD_4_parameters.ini -in FeatureLinkerUnlabeledKD_dc_input1.featureXML FeatureLinkerUnlabeledKD_dc_input2.featureXML FeatureLinkerUnlabeledKD_dc_input3.featureXML FeatureLinkerUnlabeledKD_dc_input1.featureXML FeatureLinkerUnlabeledKD_dc_input2.featureXML -out FeatureLinkerUnlabeledKD_4_output.tmp -algorithm:link:charge_merging Identical -algorithm:link:adduct_merging Any > TOPP_FeatureLinkerUnlabeledKD_4.stdout 2> TOPP_FeatureLinkerUnlabeledKD_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledKD_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledKD_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledKD_4.stdout)";fi
+FeatureLinkerUnlabeledKD -test -ini FeatureLinkerUnlabeledKD_4_parameters.ini -in FeatureLinkerUnlabeledKD_dc_input1.featureXML FeatureLinkerUnlabeledKD_dc_input2.featureXML FeatureLinkerUnlabeledKD_dc_input3.featureXML FeatureLinkerUnlabeledKD_dc_input1.featureXML FeatureLinkerUnlabeledKD_dc_input2.featureXML -out FeatureLinkerUnlabeledKD_5_output.tmp -algorithm:link:charge_merging With_charge_zero -algorithm:link:adduct_merging Any > TOPP_FeatureLinkerUnlabeledKD_5.stdout 2> TOPP_FeatureLinkerUnlabeledKD_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledKD_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledKD_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledKD_5.stdout)";fi
+FeatureLinkerUnlabeledKD -test -ini FeatureLinkerUnlabeledKD_4_parameters.ini -in FeatureLinkerUnlabeledKD_dc_input1.featureXML FeatureLinkerUnlabeledKD_dc_input2.featureXML FeatureLinkerUnlabeledKD_dc_input3.featureXML FeatureLinkerUnlabeledKD_dc_input1.featureXML FeatureLinkerUnlabeledKD_dc_input2.featureXML -out FeatureLinkerUnlabeledKD_6_output.tmp -algorithm:link:charge_merging Any -algorithm:link:adduct_merging With_unknown_adducts > TOPP_FeatureLinkerUnlabeledKD_6.stdout 2> TOPP_FeatureLinkerUnlabeledKD_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledKD_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledKD_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledKD_6.stdout)";fi
+FeatureLinkerUnlabeledKD -test -ini FeatureLinkerUnlabeledKD_4_parameters.ini -in FeatureLinkerUnlabeledKD_dc_input1.featureXML FeatureLinkerUnlabeledKD_dc_input2.featureXML FeatureLinkerUnlabeledKD_dc_input3.featureXML FeatureLinkerUnlabeledKD_dc_input1.featureXML FeatureLinkerUnlabeledKD_dc_input2.featureXML -out FeatureLinkerUnlabeledKD_7_output.tmp -algorithm:link:charge_merging Any -algorithm:link:adduct_merging Identical > TOPP_FeatureLinkerUnlabeledKD_7.stdout 2> TOPP_FeatureLinkerUnlabeledKD_7.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FeatureLinkerUnlabeledKD_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FeatureLinkerUnlabeledKD_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FeatureLinkerUnlabeledKD_7.stdout)";fi
+IDMapper -test -in IDMapper_1_input.featureXML -out IDMapper_1_output.tmp -id IDMapper_1_input.idXML -mz_measure Da -mz_tolerance 1 -ignore_charge -mz_reference precursor -feature:use_centroid_mz false > TOPP_IDMapper_1.stdout 2> TOPP_IDMapper_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMapper_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMapper_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMapper_1.stdout)";fi
+IDMapper -test -in IDMapper_2_input.consensusXML -out IDMapper_2_output.tmp -id IDMapper_2_input.idXML -mz_measure Da -mz_tolerance 1 -mz_reference precursor > TOPP_IDMapper_2.stdout 2> TOPP_IDMapper_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMapper_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMapper_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMapper_2.stdout)";fi
+IDMapper -test -in IDMapper_3_input.featureXML -out IDMapper_3_output.tmp -id IDMapper_3_input.idXML -mz_measure ppm -mz_tolerance 3 -rt_tolerance 4 -ignore_charge -mz_reference precursor > TOPP_IDMapper_3.stdout 2> TOPP_IDMapper_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMapper_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMapper_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMapper_3.stdout)";fi
+IDMapper -test -in IDMapper_4_input.featureXML -out IDMapper_4_output.tmp -id IDMapper_4_input.idXML -spectra:in IDMapper_4_input.mzML -mz_measure ppm -mz_tolerance 20 -rt_tolerance 10 > TOPP_IDMapper_4.stdout 2> TOPP_IDMapper_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMapper_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMapper_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMapper_4.stdout)";fi
+IDMapper -test -in IDMapper_5_input.featureXML -out IDMapper_5_output.tmp -id IDMapper_5_input.idXML -spectra:in IDMapper_5_input.mzML -mz_measure ppm -mz_tolerance 10 -rt_tolerance 20 -feature:use_centroid_mz false > TOPP_IDMapper_5.stdout 2> TOPP_IDMapper_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDMapper_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDMapper_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDMapper_5.stdout)";fi
+IDRipper -test -in IDRipper_1_input.idXML -out dummy.tmp > TOPP_IDRipper_1.stdout 2> TOPP_IDRipper_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDRipper_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDRipper_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDRipper_1.stdout)";fi
+IDRipper -test -in IDRipper_2_input.idXML -out_path dummy.tmp > TOPP_IDRipper_2.stdout 2> TOPP_IDRipper_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDRipper_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDRipper_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDRipper_2.stdout)";fi
+IDMerger -test -in IDRipper_3_input1.idXML IDRipper_3_input2.idXML -out IDRipper_3_output.tmp -annotate_file_origin > TOPP_IDRipper_3_prep.stdout 2> TOPP_IDRipper_3_prep.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDRipper_3_prep failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDRipper_3_prep.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDRipper_3_prep.stdout)";fi
+IDRipper -test -in IDRipper_3_output.idXML -out_path dummy2.tmp > TOPP_IDRipper_3.stdout 2> TOPP_IDRipper_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDRipper_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDRipper_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDRipper_3.stdout)";fi
+ConsensusID -test -in ConsensusID_1_input.idXML -out ConsensusID_1_output.tmp -algorithm PEPMatrix -PEPMatrix:matrix PAM30MS > TOPP_ConsensusID_1.stdout 2> TOPP_ConsensusID_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConsensusID_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConsensusID_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConsensusID_1.stdout)";fi
+ConsensusID -test -in ConsensusID_2_input.featureXML -out ConsensusID_2_output.tmp -algorithm average > TOPP_ConsensusID_2.stdout 2> TOPP_ConsensusID_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConsensusID_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConsensusID_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConsensusID_2.stdout)";fi
+ConsensusID -test -in ConsensusID_3_input.consensusXML -out ConsensusID_3_output.tmp -algorithm best > TOPP_ConsensusID_3.stdout 2> TOPP_ConsensusID_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConsensusID_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConsensusID_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConsensusID_3.stdout)";fi
+ConsensusID -test -in ConsensusID_1_input.idXML -out ConsensusID_4_output.tmp -algorithm PEPMatrix -PEPMatrix:matrix identity -filter:considered_hits 6 > TOPP_ConsensusID_4.stdout 2> TOPP_ConsensusID_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConsensusID_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConsensusID_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConsensusID_4.stdout)";fi
+ConsensusID -test -in ConsensusID_1_input.idXML -out ConsensusID_5_output.tmp -algorithm PEPIons > TOPP_ConsensusID_5.stdout 2> TOPP_ConsensusID_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConsensusID_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConsensusID_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConsensusID_5.stdout)";fi
+ConsensusID -test -in ConsensusID_1_input.idXML -out ConsensusID_6_output.tmp -algorithm best -filter:min_support 0.5 > TOPP_ConsensusID_6.stdout 2> TOPP_ConsensusID_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ConsensusID_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ConsensusID_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ConsensusID_6.stdout)";fi
+PrecursorIonSelector -test -in PrecursorIonSelector_features.featureXML -sim_results PrecursorIonSelector_1_output.tmp -ini PrecursorIonSelector_1_parameters.ini -db_path PrecursorIonSelector_db.fasta -ids PrecursorIonSelector_ids.idXML > TOPP_PrecursorIonSelector_1.stdout 2> TOPP_PrecursorIonSelector_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PrecursorIonSelector_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PrecursorIonSelector_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PrecursorIonSelector_1.stdout)";fi
+PrecursorIonSelector -test -in PrecursorIonSelector_features.featureXML -out PrecursorIonSelector_2_output.tmp -ini PrecursorIonSelector_2_parameters.ini -db_path PrecursorIonSelector_db.fasta -ids PrecursorIonSelector_ids.idXML > TOPP_PrecursorIonSelector_2.stdout 2> TOPP_PrecursorIonSelector_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PrecursorIonSelector_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PrecursorIonSelector_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PrecursorIonSelector_2.stdout)";fi
+CompNovo -test -in CompNovo_1_input.mzML -ini CompNovo_1.ini -out CompNovo_1_output.tmp > TOPP_CompNovo_1.stdout 2> TOPP_CompNovo_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_CompNovo_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_CompNovo_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_CompNovo_1.stdout)";fi
+CompNovoCID -test -in CompNovoCID_1_input.mzML -ini CompNovoCID_1.ini -out CompNovoCID_1_output.tmp > TOPP_CompNovoCID_1.stdout 2> TOPP_CompNovoCID_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_CompNovoCID_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_CompNovoCID_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_CompNovoCID_1.stdout)";fi
+PrecursorMassCorrector -test -in PrecursorMassCorrector_1_input.mzML -ini PrecursorMassCorrector_1.ini -out PrecursorMassCorrector_1_output.tmp > TOPP_PrecursorMassCorrector_1.stdout 2> TOPP_PrecursorMassCorrector_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PrecursorMassCorrector_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PrecursorMassCorrector_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PrecursorMassCorrector_1.stdout)";fi
+FalseDiscoveryRate -test -in FalseDiscoveryRate_OMSSA.idXML -out FalseDiscoveryRate_output_1.tmp -PSM true -protein false > TOPP_FalseDiscoveryRate_1.stdout 2> TOPP_FalseDiscoveryRate_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FalseDiscoveryRate_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FalseDiscoveryRate_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FalseDiscoveryRate_1.stdout)";fi
+FalseDiscoveryRate -test -in FalseDiscoveryRate_OMSSA.idXML -out FalseDiscoveryRate_output_2.tmp -algorithm:treat_runs_separately -PSM true -protein false > TOPP_FalseDiscoveryRate_2.stdout 2> TOPP_FalseDiscoveryRate_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FalseDiscoveryRate_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FalseDiscoveryRate_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FalseDiscoveryRate_2.stdout)";fi
+FalseDiscoveryRate -test -in FalseDiscoveryRate_OMSSA.idXML -out FalseDiscoveryRate_output_3.tmp -algorithm:split_charge_variants -PSM true -protein false > TOPP_FalseDiscoveryRate_3.stdout 2> TOPP_FalseDiscoveryRate_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FalseDiscoveryRate_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FalseDiscoveryRate_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FalseDiscoveryRate_3.stdout)";fi
+FalseDiscoveryRate -test -in FalseDiscoveryRate_OMSSA_4.idXML -out FalseDiscoveryRate_output_4.tmp -algorithm:split_charge_variants -PSM true -protein false > TOPP_FalseDiscoveryRate_4.stdout 2> TOPP_FalseDiscoveryRate_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FalseDiscoveryRate_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FalseDiscoveryRate_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FalseDiscoveryRate_4.stdout)";fi
+FalseDiscoveryRate -test -in FalseDiscoveryRate_5_input.idXML -out FalseDiscoveryRate_5_output.tmp -PSM false -protein true -algorithm:add_decoy_proteins -force > TOPP_FalseDiscoveryRate_5.stdout 2> TOPP_FalseDiscoveryRate_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FalseDiscoveryRate_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FalseDiscoveryRate_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FalseDiscoveryRate_5.stdout)";fi
+FalseDiscoveryRate -test -in FalseDiscoveryRate_6_input.idXML -out FalseDiscoveryRate_6_output.tmp -PSM true -protein false -FDR:PSM 0.05 > TOPP_FalseDiscoveryRate_6.stdout 2> TOPP_FalseDiscoveryRate_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FalseDiscoveryRate_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FalseDiscoveryRate_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FalseDiscoveryRate_6.stdout)";fi
+FalseDiscoveryRate -test -in FalseDiscoveryRate_7_input.idXML -out FalseDiscoveryRate_7_output.tmp -PSM false -protein true -FDR:protein 0.30 -force > TOPP_FalseDiscoveryRate_7.stdout 2> TOPP_FalseDiscoveryRate_7.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FalseDiscoveryRate_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FalseDiscoveryRate_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FalseDiscoveryRate_7.stdout)";fi
+IDPosteriorErrorProbability -test -in IDPosteriorErrorProbability_Mascot_input.idXML -out IDPosteriorErrorProbability_output_1.tmp > TOPP_IDPosteriorErrorProbability_1.stdout 2> TOPP_IDPosteriorErrorProbability_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDPosteriorErrorProbability_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDPosteriorErrorProbability_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDPosteriorErrorProbability_1.stdout)";fi
+IDPosteriorErrorProbability -test -in IDPosteriorErrorProbability_XTandem_input.idXML -out IDPosteriorErrorProbability_output_2.tmp > TOPP_IDPosteriorErrorProbability_2.stdout 2> TOPP_IDPosteriorErrorProbability_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDPosteriorErrorProbability_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDPosteriorErrorProbability_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDPosteriorErrorProbability_2.stdout)";fi
+IDPosteriorErrorProbability -test -in IDPosteriorErrorProbability_OMSSA_input.idXML -out IDPosteriorErrorProbability_output_3.tmp > TOPP_IDPosteriorErrorProbability_3.stdout 2> TOPP_IDPosteriorErrorProbability_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDPosteriorErrorProbability_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDPosteriorErrorProbability_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDPosteriorErrorProbability_3.stdout)";fi
+IDPosteriorErrorProbability -test -in IDPosteriorErrorProbability_OMSSA_input2.idXML -out IDPosteriorErrorProbability_output_4.tmp -split_charge > TOPP_IDPosteriorErrorProbability_4.stdout 2> TOPP_IDPosteriorErrorProbability_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDPosteriorErrorProbability_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDPosteriorErrorProbability_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDPosteriorErrorProbability_4.stdout)";fi
+IDPosteriorErrorProbability -test -in IDPosteriorErrorProbability_XTandem_input2.idXML -out IDPosteriorErrorProbability_output_5.tmp -split_charge > TOPP_IDPosteriorErrorProbability_5.stdout 2> TOPP_IDPosteriorErrorProbability_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDPosteriorErrorProbability_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDPosteriorErrorProbability_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDPosteriorErrorProbability_5.stdout)";fi
+IDPosteriorErrorProbability -test -in IDPosteriorErrorProbability_Mascot_input2.idXML -out IDPosteriorErrorProbability_output_6.tmp -split_charge > TOPP_IDPosteriorErrorProbability_6.stdout 2> TOPP_IDPosteriorErrorProbability_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDPosteriorErrorProbability_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDPosteriorErrorProbability_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDPosteriorErrorProbability_6.stdout)";fi
+IDPosteriorErrorProbability -test -in IDPosteriorErrorProbability_bad_data.idXML -out IDPosteriorErrorProbability_bad_data_output.tmp -ignore_bad_data > TOPP_IDPosteriorErrorProbability_7.stdout 2> TOPP_IDPosteriorErrorProbability_7.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDPosteriorErrorProbability_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDPosteriorErrorProbability_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDPosteriorErrorProbability_7.stdout)";fi
+IDPosteriorErrorProbability -test -in IDPosteriorErrorProbability_OMSSA_input.idXML -out IDPosteriorErrorProbability_output_8.tmp -prob_correct > TOPP_IDPosteriorErrorProbability_8.stdout 2> TOPP_IDPosteriorErrorProbability_8.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_IDPosteriorErrorProbability_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_IDPosteriorErrorProbability_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_IDPosteriorErrorProbability_8.stdout)";fi
+ProteinResolver -test -in ProteinResolver_1_input.consensusXML -fasta ProteinResolver_1_input.fasta -protein_groups ProteinResolver_1_output1.tmp -peptide_table ProteinResolver_1_output2.tmp -protein_table ProteinResolver_1_output3.tmp > TOPP_ProteinResolver_1.stdout 2> TOPP_ProteinResolver_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinResolver_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinResolver_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinResolver_1.stdout)";fi
+ProteinQuantifier -test -in ProteinQuantifier_input.featureXML -out ProteinQuantifier_1_output1.tmp -peptide_out ProteinQuantifier_1_output2.tmp > TOPP_ProteinQuantifier_1.stdout 2> TOPP_ProteinQuantifier_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_1.stdout)";fi
+ProteinQuantifier -test -in ProteinQuantifier_input.featureXML -out ProteinQuantifier_2_output1.tmp -peptide_out ProteinQuantifier_2_output2.tmp -top 2 -include_all -best_charge_and_fraction -average sum > TOPP_ProteinQuantifier_2.stdout 2> TOPP_ProteinQuantifier_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_2.stdout)";fi
+ProteinQuantifier -test -in ProteinQuantifier_3_input.featureXML -out ProteinQuantifier_3_output1.tmp -peptide_out ProteinQuantifier_3_output2.tmp -top 2 -include_all -average mean > TOPP_ProteinQuantifier_3.stdout 2> TOPP_ProteinQuantifier_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_3.stdout)";fi
+ProteinQuantifier -test -in ProteinQuantifier_input.consensusXML -out ProteinQuantifier_4_output.tmp -top 0 -average sum > TOPP_ProteinQuantifier_4.stdout 2> TOPP_ProteinQuantifier_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_4.stdout)";fi
+ProteinQuantifier -test -in ProteinQuantifier_input.consensusXML -out ProteinQuantifier_5_output.tmp -top 3 -average sum > TOPP_ProteinQuantifier_5.stdout 2> TOPP_ProteinQuantifier_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_5.stdout)";fi
+ProteinQuantifier -test -in ProteinQuantifier_input.consensusXML -out ProteinQuantifier_6_output.tmp -top 3 -include_all -average sum > TOPP_ProteinQuantifier_6.stdout 2> TOPP_ProteinQuantifier_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_6.stdout)";fi
+ProteinQuantifier -test -in ProteinQuantifier_input.consensusXML -out ProteinQuantifier_7_output.tmp -top 0 -consensus:fix_peptides -average sum > TOPP_ProteinQuantifier_7.stdout 2> TOPP_ProteinQuantifier_7.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_7.stdout)";fi
+ProteinQuantifier -test -in ProteinQuantifier_input.consensusXML -out ProteinQuantifier_8_output.tmp -top 3 -consensus:fix_peptides -average sum > TOPP_ProteinQuantifier_8.stdout 2> TOPP_ProteinQuantifier_8.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_8.stdout)";fi
+ProteinQuantifier -test -in ProteinQuantifier_input.consensusXML -out ProteinQuantifier_9_output.tmp -top 3 -include_all -consensus:fix_peptides -average sum > TOPP_ProteinQuantifier_9.stdout 2> TOPP_ProteinQuantifier_9.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_9.stdout)";fi
+ProteinQuantifier -test -in ProteinQuantifier_input.consensusXML -out ProteinQuantifier_12_output.tmp -top 3 -include_all -consensus:fix_peptides -average sum -ratios > TOPP_ProteinQuantifier_12.stdout 2> TOPP_ProteinQuantifier_12.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_12 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_12.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_12.stdout)";fi
+ProteinQuantifier -test -in ProteinQuantifier_input.consensusXML -out ProteinQuantifier_13_output.tmp -top 3 -include_all -consensus:fix_peptides -average sum -ratiosSILAC > TOPP_ProteinQuantifier_13.stdout 2> TOPP_ProteinQuantifier_13.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_13 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_13.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_13.stdout)";fi
+ProteinQuantifier -test -in ProteinQuantifier_input.idXML -out ProteinQuantifier_14_output1.tmp -peptide_out ProteinQuantifier_14_output2.tmp -top 0 -average sum > TOPP_ProteinQuantifier_14.stdout 2> TOPP_ProteinQuantifier_14.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_ProteinQuantifier_14 failed'; >&2 echo -e "stderr:\n$(cat TOPP_ProteinQuantifier_14.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_ProteinQuantifier_14.stdout)";fi
+InclusionExclusionListCreator -test -include InclusionExclusionListCreator.featureXML -out InclusionExclusionListCreator_1_output.tmp > TOPP_InclusionExclusionListCreator_1.stdout 2> TOPP_InclusionExclusionListCreator_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InclusionExclusionListCreator_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_InclusionExclusionListCreator_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InclusionExclusionListCreator_1.stdout)";fi
+InclusionExclusionListCreator -test -exclude InclusionExclusionListCreator.featureXML -out InclusionExclusionListCreator_2_output.tmp -ini InclusionExclusionListCreator_2.ini > TOPP_InclusionExclusionListCreator_2.stdout 2> TOPP_InclusionExclusionListCreator_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InclusionExclusionListCreator_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_InclusionExclusionListCreator_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InclusionExclusionListCreator_2.stdout)";fi
+InclusionExclusionListCreator -test -include InclusionExclusionListCreator.fasta -out InclusionExclusionListCreator_3_output.tmp -inclusion_charges 1 2 -rt_model InclusionExclusionListCreator_rt.model > TOPP_InclusionExclusionListCreator_3.stdout 2> TOPP_InclusionExclusionListCreator_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InclusionExclusionListCreator_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_InclusionExclusionListCreator_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InclusionExclusionListCreator_3.stdout)";fi
+InclusionExclusionListCreator -test -exclude InclusionExclusionListCreator.fasta -out InclusionExclusionListCreator_4_output.tmp -exclusion_charges 1 2 -rt_model InclusionExclusionListCreator_rt.model -ini InclusionExclusionListCreator_4.ini > TOPP_InclusionExclusionListCreator_4.stdout 2> TOPP_InclusionExclusionListCreator_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InclusionExclusionListCreator_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_InclusionExclusionListCreator_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InclusionExclusionListCreator_4.stdout)";fi
+InclusionExclusionListCreator -test -exclude InclusionExclusionListCreator.idXML -out InclusionExclusionListCreator_5_output.tmp -exclusion_charges 1 2 -rt_model InclusionExclusionListCreator_rt.model > TOPP_InclusionExclusionListCreator_5.stdout 2> TOPP_InclusionExclusionListCreator_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InclusionExclusionListCreator_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_InclusionExclusionListCreator_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InclusionExclusionListCreator_5.stdout)";fi
+InclusionExclusionListCreator -test -exclude InclusionExclusionListCreator.idXML -out InclusionExclusionListCreator_6_output.tmp -exclusion_charges 1 2 -rt_model InclusionExclusionListCreator_rt.model -ini InclusionExclusionListCreator_6.ini > TOPP_InclusionExclusionListCreator_6.stdout 2> TOPP_InclusionExclusionListCreator_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_InclusionExclusionListCreator_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_InclusionExclusionListCreator_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_InclusionExclusionListCreator_6.stdout)";fi
+PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in PeptideIndexer_1.idXML -out PeptideIndexer_1_out.tmp.idXML -allow_unmatched -enzyme:specificity none -aaa_max 4 > TOPP_PeptideIndexer_1.stdout 2> TOPP_PeptideIndexer_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_1.stdout)";fi
+PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in PeptideIndexer_1.idXML -out PeptideIndexer_2_out.tmp.idXML -allow_unmatched -write_protein_sequence -enzyme:specificity none -aaa_max 4 > TOPP_PeptideIndexer_2.stdout 2> TOPP_PeptideIndexer_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_2.stdout)";fi
+PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in PeptideIndexer_1.idXML -out PeptideIndexer_3_out.tmp.idXML -allow_unmatched -keep_unreferenced_proteins -enzyme:specificity none -aaa_max 4 > TOPP_PeptideIndexer_3.stdout 2> TOPP_PeptideIndexer_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_3.stdout)";fi
+PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in PeptideIndexer_1.idXML -out PeptideIndexer_4_out.tmp.idXML -allow_unmatched -aaa_max 0 -write_protein_sequence -enzyme:specificity none -aaa_max 4 > TOPP_PeptideIndexer_4.stdout 2> TOPP_PeptideIndexer_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_4.stdout)";fi
+PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in PeptideIndexer_1.idXML -out PeptideIndexer_5_out.tmp.idXML -allow_unmatched -enzyme:specificity none -aaa_max 4 > TOPP_PeptideIndexer_5.stdout 2> TOPP_PeptideIndexer_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_5.stdout)";fi
+PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in PeptideIndexer_2.idXML -out PeptideIndexer_6_out.tmp.idXML -allow_unmatched -enzyme:specificity none -aaa_max 3 > TOPP_PeptideIndexer_6.stdout 2> TOPP_PeptideIndexer_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_6.stdout)";fi
+PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in PeptideIndexer_3.idXML -out PeptideIndexer_7_out.tmp.idXML -allow_unmatched -aaa_max 4 -decoy_string DECOY_ > TOPP_PeptideIndexer_7.stdout 2> TOPP_PeptideIndexer_7.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_7.stdout)";fi
+PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in PeptideIndexer_3.idXML -out PeptideIndexer_8_out.tmp.idXML -allow_unmatched -enzyme:specificity semi -aaa_max 4 > TOPP_PeptideIndexer_8.stdout 2> TOPP_PeptideIndexer_8.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_8.stdout)";fi
+PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in PeptideIndexer_3.idXML -out PeptideIndexer_9_out.tmp.idXML -allow_unmatched -enzyme:specificity none -aaa_max 4 > TOPP_PeptideIndexer_9.stdout 2> TOPP_PeptideIndexer_9.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_9 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_9.stdout)";fi
+PeptideIndexer -test -fasta PeptideIndexer_10_input.fasta -in PeptideIndexer_10_input.idXML -out PeptideIndexer_10_output.tmp.idXML -IL_equivalent -aaa_max 3 -write_protein_sequence > TOPP_PeptideIndexer_10.stdout 2> TOPP_PeptideIndexer_10.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_10 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_10.stdout)";fi
+PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in PeptideIndexer_1.idXML -out PeptideIndexer_12_out.tmp.idXML -allow_unmatched -enzyme:specificity none -aaa_max 4 > TOPP_PeptideIndexer_12.stdout 2> TOPP_PeptideIndexer_12.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_12 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_12.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_12.stdout)";fi
+PeptideIndexer -test -fasta PeptideIndexer_1.fasta -in empty.idXML -out PeptideIndexer_13_out.tmp.idXML -aaa_max 4 > TOPP_PeptideIndexer_13.stdout 2> TOPP_PeptideIndexer_13.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_13 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_13.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_13.stdout)";fi
+PeptideIndexer -test -fasta PeptideIndexer_2.fasta -in PeptideIndexer_14.idXML -out PeptideIndexer_14_out.tmp.idXML -enzyme:specificity none -aaa_max 4 -write_protein_sequence > TOPP_PeptideIndexer_14.stdout 2> TOPP_PeptideIndexer_14.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PeptideIndexer_14 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PeptideIndexer_14.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PeptideIndexer_14.stdout)";fi
+MzTabExporter -test -in MzTabExporter_1_input.consensusXML -out MzTabExporter_1_output.tmp > TOPP_MzTabExporter_1.stdout 2> TOPP_MzTabExporter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MzTabExporter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MzTabExporter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MzTabExporter_1.stdout)";fi
+MzTabExporter -test -in MzTabExporter_2_input.idXML -out MzTabExporter_2_output.tmp > TOPP_MzTabExporter_2.stdout 2> TOPP_MzTabExporter_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MzTabExporter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MzTabExporter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MzTabExporter_2.stdout)";fi
+MzTabExporter -test -in MzTabExporter_3_input.featureXML -out MzTabExporter_3_output.tmp > TOPP_MzTabExporter_3.stdout 2> TOPP_MzTabExporter_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MzTabExporter_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MzTabExporter_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MzTabExporter_3.stdout)";fi
+OpenPepXL -test -decoy_string "decoy" -in OpenPepXL_input.mzML -consensus OpenPepXL_input.consensusXML -database OpenPepXL_input.fasta -out_xquestxml OpenPepXL_output.xquest.xml.tmp -out_xquest_specxml OpenPepXL_output.spec.xml.tmp -out_mzIdentML OpenPepXL_output.mzid.tmp -out_idXML OpenPepXL_output.idXML.tmp > TOPP_OpenPepXL_1.stdout 2> TOPP_OpenPepXL_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenPepXL_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenPepXL_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenPepXL_1.stdout)";fi
+OpenPepXLLF -test -decoy_string "decoy" -in OpenPepXLLF_input.mzML -database OpenPepXLLF_input.fasta -out_xquestxml OpenPepXLLF_output.xquest.xml.tmp -out_xquest_specxml OpenPepXLLF_output.spec.xml.tmp -out_mzIdentML OpenPepXLLF_output.mzid.tmp -out_idXML OpenPepXLLF_output.idXML.tmp > TOPP_OpenPepXLLF_1.stdout 2> TOPP_OpenPepXLLF_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenPepXLLF_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenPepXLLF_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenPepXLLF_1.stdout)";fi
+OpenPepXLLF -test -ini OpenPepXLLF_input2.ini -in OpenPepXLLF_input2.mzML -database OpenPepXLLF_input2.fasta -out_idXML OpenPepXLLF_output2.idXML.tmp > TOPP_OpenPepXLLF_2.stdout 2> TOPP_OpenPepXLLF_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OpenPepXLLF_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OpenPepXLLF_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OpenPepXLLF_2.stdout)";fi
+XFDR -test -binsize 0.1 -in XFDR_test_in1.idXML -out_idXML XFDR_test_out1_temp.idXML -out_mzIdentML XFDR_test_out1_temp.mzid -out_xquest XFDR_test_out1_temp.xquest.xml > TOPP_XFDR_1.stdout 2> TOPP_XFDR_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_XFDR_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_XFDR_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_XFDR_1.stdout)";fi
+XFDR -test -binsize 0.1 -in XFDR_test_in1.idXML -uniquexl -no_qvalues -out_idXML XFDR_test_out2_temp.idXML -out_mzIdentML XFDR_test_out2_temp.mzid -out_xquest XFDR_test_out2_temp.xquest.xml > TOPP_XFDR_2.stdout 2> TOPP_XFDR_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_XFDR_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_XFDR_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_XFDR_2.stdout)";fi
+XFDR -test -binsize 0.1 -minscore 0.0 -in XFDR_test_in2.xquest.xml -out_idXML XFDR_test_out3_temp.idXML -out_mzIdentML XFDR_test_out3_temp.mzid -out_xquest XFDR_test_out3_temp.xquest.xml > TOPP_XFDR_3.stdout 2> TOPP_XFDR_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_XFDR_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_XFDR_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_XFDR_3.stdout)";fi
+XFDR -test -binsize 0.1 -minborder -3 -maxborder 3 -in XFDR_test_in2.xquest.xml -out_idXML XFDR_test_out4_temp.idXML -out_mzIdentML XFDR_test_out4_temp.mzid -out_xquest XFDR_test_out4_temp.xquest.xml > TOPP_XFDR_4.stdout 2> TOPP_XFDR_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_XFDR_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_XFDR_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_XFDR_4.stdout)";fi
+XFDR -test -binsize 0.1 -minborder -3 -maxborder 3 -in XFDR_test_in3.xquest.xml -out_idXML XFDR_test_out5_temp.idXML -out_mzIdentML XFDR_test_out5_temp.mzid -out_xquest XFDR_test_out5_temp.xquest.xml > TOPP_XFDR_5.stdout 2> TOPP_XFDR_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_XFDR_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_XFDR_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_XFDR_5.stdout)";fi
+XFDR -test -binsize 0.1 -in XFDR_test_in4.idXML -out_idXML XFDR_test_out6_temp.idXML > TOPP_XFDR_6.stdout 2> TOPP_XFDR_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_XFDR_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_XFDR_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_XFDR_6.stdout)";fi
+XFDR -test -uniquexl -binsize 0.1 -minscore 0.0 -in XFDR_test_in2.xquest.xml -out_idXML XFDR_test_out7_temp.idXML -out_mzIdentML XFDR_test_out7_temp.mzid -out_xquest XFDR_test_out7_temp.xquest.xml > TOPP_XFDR_7.stdout 2> TOPP_XFDR_7.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_XFDR_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_XFDR_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_XFDR_7.stdout)";fi
+QualityControl -test -in_raw QualityControl_1_in1.mzML.gz QualityControl_1_in2.mzML.gz QualityControl_1_in3.mzML.gz -in_postFDR QualityControl_1_in1.featureXML QualityControl_1_in2.featureXML QualityControl_1_in3.featureXML -in_trafo QualityControl_1_in1.trafoXML QualityControl_1_in2.trafoXML QualityControl_1_in3.trafoXML -in_contaminants QualityControl_1.fasta -in_cm QualityControl_1_in.consensusXML -out_cm QualityControl_1_out.consensusXML.tmp -out QualityControl_1_out.mzTab.tmp > TOPP_QualityControl_1.stdout 2> TOPP_QualityControl_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_QualityControl_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_QualityControl_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_QualityControl_1.stdout)";fi
+AccurateMassSearch -test -in ConsensusMapNormalizer_input.consensusXML -out AccurateMassSearch_1_output.tmp.mzTab > UTILS_AccurateMassSearch_1.stdout 2> UTILS_AccurateMassSearch_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AccurateMassSearch_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AccurateMassSearch_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AccurateMassSearch_1.stdout)";fi
+AccurateMassSearch -test -in AccurateMassSearch_2_input.featureXML -out AccurateMassSearch_2_output.tmp.mzTab -out_annotation AccurateMassSearch_2_output.tmp.featureXML -db:mapping AMS_test_Mapping.tsv -db:struct AMS_test_Struct.tsv -positive_adducts AMS_PositiveAdducts.tsv -negative_adducts AMS_NegativeAdducts.tsv -algorithm:mzTab:exportIsotopeIntensities true > UTILS_AccurateMassSearch_2.stdout 2> UTILS_AccurateMassSearch_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AccurateMassSearch_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AccurateMassSearch_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AccurateMassSearch_2.stdout)";fi
+AccurateMassSearch -test -in AccurateMassSearch_2_input.featureXML -out AccurateMassSearch_3_output.tmp.mzTab -out_annotation AccurateMassSearch_2_output.tmp.featureXML -db:mapping AMS_test_Mapping.tsv -db:struct AMS_test_Struct.tsv -positive_adducts AMS_PositiveAdducts.tsv -negative_adducts AMS_NegativeAdducts.tsv > UTILS_AccurateMassSearch_3.stdout 2> UTILS_AccurateMassSearch_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AccurateMassSearch_3 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AccurateMassSearch_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AccurateMassSearch_3.stdout)";fi
+AssayGeneratorMetabo -test -in AssayGeneratorMetabo_input.mzML -in_id AssayGeneratorMetabo_ffm_input.featureXML -out AssayGeneratorMetabo_ffm_output.tmp.tsv -min_transitions 1 > UTILS_AssayGeneratorMetabo_1.stdout 2> UTILS_AssayGeneratorMetabo_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AssayGeneratorMetabo_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AssayGeneratorMetabo_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AssayGeneratorMetabo_1.stdout)";fi
+AssayGeneratorMetabo -test -in AssayGeneratorMetabo_input.mzML -in_id AssayGeneratorMetabo_ams_input.featureXML -out AssayGeneratorMetabo_ams_output.tmp.tsv -min_transitions 1 > UTILS_AssayGeneratorMetabo_2.stdout 2> UTILS_AssayGeneratorMetabo_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AssayGeneratorMetabo_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AssayGeneratorMetabo_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AssayGeneratorMetabo_2.stdout)";fi
+AssayGeneratorMetabo -test -in AssayGeneratorMetabo_input.mzML -in_id AssayGeneratorMetabo_ffm_input.featureXML -out AssayGeneratorMetabo_ffm_output_consensus.tmp.tsv -method consensus_spectrum -min_transitions 1 > UTILS_AssayGeneratorMetabo_3.stdout 2> UTILS_AssayGeneratorMetabo_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AssayGeneratorMetabo_3 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AssayGeneratorMetabo_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AssayGeneratorMetabo_3.stdout)";fi
+AssayGeneratorMetabo -test -in AssayGeneratorMetabo_input.mzML -in_id AssayGeneratorMetabo_ams_input.featureXML -out AssayGeneratorMetabo_ams_output_consensus.tmp.tsv -method consensus_spectrum -min_transitions 1 > UTILS_AssayGeneratorMetabo_4.stdout 2> UTILS_AssayGeneratorMetabo_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AssayGeneratorMetabo_4 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AssayGeneratorMetabo_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AssayGeneratorMetabo_4.stdout)";fi
+AssayGeneratorMetabo -test -in AssayGeneratorMetabo_input.mzML -in_id AssayGeneratorMetabo_ams_input.featureXML -out AssayGeneratorMetabo_ams_uku_output_consensus.tmp.tsv -method consensus_spectrum -use_known_unknowns -min_transitions 1 > UTILS_AssayGeneratorMetabo_5.stdout 2> UTILS_AssayGeneratorMetabo_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AssayGeneratorMetabo_5 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AssayGeneratorMetabo_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AssayGeneratorMetabo_5.stdout)";fi
+TargetedFileConverter -test -in AssayGeneratorMetabo_ams_uku_output_consensus.tsv -out AssayGeneratorMetabo_ams_uku_output_consensus_traml.tmp.TraML > UTILS_AssayGeneratorMetabo_6.stdout 2> UTILS_AssayGeneratorMetabo_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AssayGeneratorMetabo_6 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AssayGeneratorMetabo_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AssayGeneratorMetabo_6.stdout)";fi
+ImageCreator -test -in ImageCreator_1_input.mzML -out ImageCreator1.bmp -width 20 -height 15 > UTILS_ImageCreator_1.stdout 2> UTILS_ImageCreator_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_ImageCreator_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_ImageCreator_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_ImageCreator_1.stdout)";fi
+ImageCreator -test -in ImageCreator_2_input.mzML -out ImageCreator2.png -out_type bmp -width 20 -height 15 -precursors -precursor_size 3 -precursor_color green -log_intensity > UTILS_ImageCreator_2.stdout 2> UTILS_ImageCreator_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_ImageCreator_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_ImageCreator_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_ImageCreator_2.stdout)";fi
+IDScoreSwitcher -test -in IDFileConverter_12_output.idXML -out IDScoreSwitcher_1_output.tmp -new_score Percolator_PEP -new_score_type "Posterior Error Probability" -new_score_orientation lower_better -old_score Percolator_qvalue > UTILS_IDScoreSwitcher_1.stdout 2> UTILS_IDScoreSwitcher_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_IDScoreSwitcher_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_IDScoreSwitcher_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_IDScoreSwitcher_1.stdout)";fi
+IDScoreSwitcher -test -in IDScoreSwitcher_2_input.idXML -out IDScoreSwitcher_2_output.tmp -new_score "Posterior Probability_score" -new_score_type "Posterior Probability" -new_score_orientation higher_better -proteins > UTILS_IDScoreSwitcher_2.stdout 2> UTILS_IDScoreSwitcher_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_IDScoreSwitcher_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_IDScoreSwitcher_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_IDScoreSwitcher_2.stdout)";fi
+IDSplitter -test -in IDMapper_1_output.featureXML -out IDSplitter_1_output1.tmp -id_out IDSplitter_1_output2.tmp > UTILS_IDSplitter_1.stdout 2> UTILS_IDSplitter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_IDSplitter_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_IDSplitter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_IDSplitter_1.stdout)";fi
+MassCalculator -test -in MassCalculator_1_input.txt -out MassCalculator_1_output.tmp -charge 0 1 -format table -separator , > UTILS_MassCalculator_1.stdout 2> UTILS_MassCalculator_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_MassCalculator_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_MassCalculator_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_MassCalculator_1.stdout)";fi
+MassCalculator -test -in_seq "LDQWLC(Carbamidomethyl)EKL" "(Glu->pyro-Glu)EAM(Oxidation)APKHK" "RANVM(Oxidation)DYR" "FGVEQDVDMVFASFIR" -out MassCalculator_2_output.tmp -charge 1 2 3 > UTILS_MassCalculator_2.stdout 2> UTILS_MassCalculator_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_MassCalculator_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_MassCalculator_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_MassCalculator_2.stdout)";fi
+MultiplexResolver -test -in MultiplexResolver_1_input.consensusXML -ini MultiplexResolver_1_parameters.ini -out MultiplexResolver_1.tmp -out_conflicts MultiplexResolver_1_conflicts.tmp > UTILS_MultiplexResolver_1.stdout 2> UTILS_MultiplexResolver_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_MultiplexResolver_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_MultiplexResolver_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_MultiplexResolver_1.stdout)";fi
+MultiplexResolver -test -in MultiplexResolver_2_input.consensusXML -ini MultiplexResolver_2_parameters.ini -out MultiplexResolver_2.tmp -out_conflicts MultiplexResolver_2_conflicts.tmp > UTILS_MultiplexResolver_2.stdout 2> UTILS_MultiplexResolver_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_MultiplexResolver_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_MultiplexResolver_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_MultiplexResolver_2.stdout)";fi
+MultiplexResolver -test -in MultiplexResolver_3_input.consensusXML -ini MultiplexResolver_3_parameters.ini -out MultiplexResolver_3.tmp -out_conflicts MultiplexResolver_3_conflicts.tmp > UTILS_MultiplexResolver_3.stdout 2> UTILS_MultiplexResolver_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_MultiplexResolver_3 failed'; >&2 echo -e "stderr:\n$(cat UTILS_MultiplexResolver_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_MultiplexResolver_3.stdout)";fi
+MultiplexResolver -test -in MultiplexResolver_4_input.consensusXML -in_blacklist MultiplexResolver_4_input.mzML -ini MultiplexResolver_4_parameters.ini -out MultiplexResolver_4.tmp -out_conflicts MultiplexResolver_4_conflicts.tmp > UTILS_MultiplexResolver_4.stdout 2> UTILS_MultiplexResolver_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_MultiplexResolver_4 failed'; >&2 echo -e "stderr:\n$(cat UTILS_MultiplexResolver_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_MultiplexResolver_4.stdout)";fi
+INIUpdater -test -in INIUpdater_1_noupdate.toppas -out INIUpdater_1_noupdate.toppas.tmp > UTILS_INIUpdater_1.stdout 2> UTILS_INIUpdater_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_INIUpdater_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_INIUpdater_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_INIUpdater_1.stdout)";fi
+INIUpdater -test -in INIUpdater_3_old.toppas -out INIUpdater_3_old.toppas.tmp > UTILS_INIUpdater_3.stdout 2> UTILS_INIUpdater_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_INIUpdater_3 failed'; >&2 echo -e "stderr:\n$(cat UTILS_INIUpdater_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_INIUpdater_3.stdout)";fi
+DatabaseFilter -test -in DatabaseFilter_1.fasta -id DatabaseFilter_1.idXML -out DatabaseFilter_1_out.fasta.tmp > UTILS_DatabaseFilter_1.stdout 2> UTILS_DatabaseFilter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_DatabaseFilter_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_DatabaseFilter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_DatabaseFilter_1.stdout)";fi
+DatabaseFilter -test -in DatabaseFilter_1.fasta -id DatabaseFilter_1.idXML -out DatabaseFilter_2_out.fasta.tmp -method blacklist > UTILS_DatabaseFilter_2.stdout 2> UTILS_DatabaseFilter_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_DatabaseFilter_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_DatabaseFilter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_DatabaseFilter_2.stdout)";fi
+DatabaseFilter -test -in DatabaseFilter_3.fasta -id DatabaseFilter_3.mzid -out DatabaseFilter_3_out.fasta.tmp > UTILS_DatabaseFilter_3.stdout 2> UTILS_DatabaseFilter_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_DatabaseFilter_3 failed'; >&2 echo -e "stderr:\n$(cat UTILS_DatabaseFilter_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_DatabaseFilter_3.stdout)";fi
+DatabaseFilter -test -in DatabaseFilter_3.fasta -id DatabaseFilter_3.mzid -out DatabaseFilter_4_out.fasta.tmp -method blacklist > UTILS_DatabaseFilter_4.stdout 2> UTILS_DatabaseFilter_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_DatabaseFilter_4 failed'; >&2 echo -e "stderr:\n$(cat UTILS_DatabaseFilter_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_DatabaseFilter_4.stdout)";fi
+DecoyDatabase -test -in DecoyDatabase_1.fasta -out DecoyDatabase_1.fasta.tmp -only_decoy > UTILS_DecoyDatabase_1.stdout 2> UTILS_DecoyDatabase_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_DecoyDatabase_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_DecoyDatabase_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_DecoyDatabase_1.stdout)";fi
+DecoyDatabase -test -in DecoyDatabase_1.fasta -out DecoyDatabase_2.fasta.tmp -decoy_string "blabla" -decoy_string_position "prefix" -method shuffle -Decoy:non_shuffle_pattern "KRP" -seed 42 > UTILS_DecoyDatabase_2.stdout 2> UTILS_DecoyDatabase_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_DecoyDatabase_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_DecoyDatabase_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_DecoyDatabase_2.stdout)";fi
+DecoyDatabase -test -in DecoyDatabase_1.fasta -out DecoyDatabase_3.fasta.tmp -decoy_string "blabla" -decoy_string_position "prefix" -method shuffle -Decoy:non_shuffle_pattern "KR" -seed 42 -enzyme "Chymotrypsin" > UTILS_DecoyDatabase_3.stdout 2> UTILS_DecoyDatabase_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_DecoyDatabase_3 failed'; >&2 echo -e "stderr:\n$(cat UTILS_DecoyDatabase_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_DecoyDatabase_3.stdout)";fi
+DecoyDatabase -test -type RNA -in DecoyDatabase_4.fasta -out DecoyDatabase_4.fasta.tmp -decoy_string "blabla" -decoy_string_position "prefix" -method reverse -seed 42 > UTILS_DecoyDatabase_4.stdout 2> UTILS_DecoyDatabase_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_DecoyDatabase_4 failed'; >&2 echo -e "stderr:\n$(cat UTILS_DecoyDatabase_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_DecoyDatabase_4.stdout)";fi
+SimpleSearchEngine -test -ini SimpleSearchEngine_1.ini -in SimpleSearchEngine_1.mzML -out SimpleSearchEngine_1_out.tmp -database SimpleSearchEngine_1.fasta > UTILS_SimpleSearchEngine_1.stdout 2> UTILS_SimpleSearchEngine_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_SimpleSearchEngine_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_SimpleSearchEngine_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_SimpleSearchEngine_1.stdout)";fi
+FeatureFinderMetaboIdent -test -in FeatureFinderMetaboIdent_1_input.mzML -id FeatureFinderMetaboIdent_1_input.tsv -out FeatureFinderMetaboIdent_1_output.tmp -extract:mz_window 5 -extract:rt_window 20 -detect:peak_width 3 > UTILS_FeatureFinderMetaboIdent_1.stdout 2> UTILS_FeatureFinderMetaboIdent_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_FeatureFinderMetaboIdent_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_FeatureFinderMetaboIdent_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_FeatureFinderMetaboIdent_1.stdout)";fi
+FeatureFinderSuperHirn -test -in FeatureFinderSuperHirn_input_1.mzML -out FeatureFinderSuperHirn_1_output.featureXML.tmp -ini FeatureFinderSuperHirn_1_parameters.ini > UTILS_FeatureFinderSuperHirn_1.stdout 2> UTILS_FeatureFinderSuperHirn_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_FeatureFinderSuperHirn_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_FeatureFinderSuperHirn_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_FeatureFinderSuperHirn_1.stdout)";fi
+FeatureFinderSuperHirn -test -in FeatureFinderSuperHirn_input_2.mzML -out FeatureFinderSuperHirn_2_output.featureXML.tmp -ini FeatureFinderSuperHirn_2_parameters.ini > UTILS_FeatureFinderSuperHirn_2.stdout 2> UTILS_FeatureFinderSuperHirn_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_FeatureFinderSuperHirn_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_FeatureFinderSuperHirn_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_FeatureFinderSuperHirn_2.stdout)";fi
+MzMLSplitter -test -in FileFilter_1_input.mzML -out MzMLSplitter_1_output -parts 2 > UTILS_MzMLSplitter_1.stdout 2> UTILS_MzMLSplitter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_MzMLSplitter_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_MzMLSplitter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_MzMLSplitter_1.stdout)";fi
+MzMLSplitter -test -in FileFilter_1_input.mzML -out MzMLSplitter_2_output -size 40 -unit KB > UTILS_MzMLSplitter_2.stdout 2> UTILS_MzMLSplitter_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_MzMLSplitter_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_MzMLSplitter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_MzMLSplitter_2.stdout)";fi
+TICCalculator -test -in MapNormalizer_output.mzML -read_method regular > UTILS_TICCalculator_1.stdout 2> UTILS_TICCalculator_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_TICCalculator_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_TICCalculator_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_TICCalculator_1.stdout)";fi
+TICCalculator -test -in MapNormalizer_output.mzML -read_method streaming -loadData true > UTILS_TICCalculator_2.stdout 2> UTILS_TICCalculator_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_TICCalculator_2 failed'; >&2 echo -e "stderr:\n$(cat UTILS_TICCalculator_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_TICCalculator_2.stdout)";fi
+TICCalculator -test -in MapNormalizer_output.mzML -read_method streaming -loadData false > UTILS_TICCalculator_3.stdout 2> UTILS_TICCalculator_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_TICCalculator_3 failed'; >&2 echo -e "stderr:\n$(cat UTILS_TICCalculator_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_TICCalculator_3.stdout)";fi
+TICCalculator -test -in MapNormalizer_output.mzML -read_method indexed > UTILS_TICCalculator_4.stdout 2> UTILS_TICCalculator_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_TICCalculator_4 failed'; >&2 echo -e "stderr:\n$(cat UTILS_TICCalculator_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_TICCalculator_4.stdout)";fi
+TICCalculator -test -in MapNormalizer_output.mzML -read_method indexed_parallel > UTILS_TICCalculator_5.stdout 2> UTILS_TICCalculator_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_TICCalculator_5 failed'; >&2 echo -e "stderr:\n$(cat UTILS_TICCalculator_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_TICCalculator_5.stdout)";fi
+ProteomicsLFQ -in examples/FRACTIONS/BSA1_F1.mzML examples/FRACTIONS/BSA1_F2.mzML examples/FRACTIONS/BSA2_F1.mzML examples/FRACTIONS/BSA2_F2.mzML examples/FRACTIONS/BSA3_F1.mzML examples/FRACTIONS/BSA3_F2.mzML -ids examples/FRACTIONS/BSA1_F1.idXML examples/FRACTIONS/BSA1_F2.idXML examples/FRACTIONS/BSA2_F1.idXML examples/FRACTIONS/BSA2_F2.idXML examples/FRACTIONS/BSA3_F1.idXML examples/FRACTIONS/BSA3_F2.idXML -design examples/FRACTIONS/BSA_design.tsv -Alignment:max_rt_shift 0 -fasta examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta -targeted_only true -transfer_ids false -mass_recalibration false -out_cxml BSA.consensusXML.tmp -out_msstats BSA.csv.tmp -out BSA.mzTab.tmp -threads 4 -proteinFDR 0.3 -test > UTILS_ProteomicsLFQ_1.stdout 2> UTILS_ProteomicsLFQ_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_ProteomicsLFQ_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_ProteomicsLFQ_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_ProteomicsLFQ_1.stdout)";fi
+NucleicAcidSearchEngine -test -ini NucleicAcidSearchEngine_1.ini -in NucleicAcidSearchEngine_1.mzML -id_out NucleicAcidSearchEngine_11_out.tmp -out NucleicAcidSearchEngine_12_out.tmp -database NucleicAcidSearchEngine_1.fasta > UTILS_NucleicAcidSearchEngine_1.stdout 2> UTILS_NucleicAcidSearchEngine_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_NucleicAcidSearchEngine_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_NucleicAcidSearchEngine_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_NucleicAcidSearchEngine_1.stdout)";fi
+RNAMassCalculator -test -in_seq "AUCGGC" -charge -1 -2 -out RNAMassCalculator.tmp > UTILS_RNAMassCalculator_1.stdout 2> UTILS_RNAMassCalculator_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_RNAMassCalculator_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_RNAMassCalculator_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_RNAMassCalculator_1.stdout)";fi
+Epifany -test -in FidoAdapter_1_input.idXML -algorithm:model_parameters:prot_prior 0.7 -algorithm:model_parameters:pep_spurious_emission 0.001 -algorithm:model_parameters:pep_emission 0.1 -out Epifany_1_out.tmp > UTILS_Epifany_1.stdout 2> UTILS_Epifany_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_Epifany_1 failed'; >&2 echo -e "stderr:\n$(cat UTILS_Epifany_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_Epifany_1.stdout)";fi
+OMSSAAdapter -test -ini OMSSAAdapter_1.ini -database proteins.fasta -in spectra.mzML -out OMSSAAdapter_1_out.tmp -omssa_executable "${OMSSA_BINARY}" > TOPP_OMSSAAdapter_1.stdout 2> TOPP_OMSSAAdapter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_OMSSAAdapter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_OMSSAAdapter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_OMSSAAdapter_1.stdout)";fi
+XTandemAdapter -test -ini XTandemAdapter_1.ini -database proteins.fasta -in spectra.mzML -out XTandemAdapter_1_out.tmp -xtandem_executable "${XTANDEM_BINARY}" > TOPP_XTandemAdapter_1.stdout 2> TOPP_XTandemAdapter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_XTandemAdapter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_XTandemAdapter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_XTandemAdapter_1.stdout)";fi
+XTandemAdapter -test -ini XTandemAdapter_1.ini -database proteins.fasta -in spectra.mzML -out XTandemAdapter_2_out.tmp -output_results valid -xtandem_executable "${XTANDEM_BINARY}" -max_valid_expect 1e-14 > TOPP_XTandemAdapter_2.stdout 2> TOPP_XTandemAdapter_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_XTandemAdapter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_XTandemAdapter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_XTandemAdapter_2.stdout)";fi
+MyriMatchAdapter -test -ini MyriMatchAdapter_1.ini -database proteins.fasta -in spectra.mzML -out MyriMatchAdapter_1_out.tmp -myrimatch_executable "${MYRIMATCH_BINARY}" > TOPP_MyriMatchAdapter_1.stdout 2> TOPP_MyriMatchAdapter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MyriMatchAdapter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MyriMatchAdapter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MyriMatchAdapter_1.stdout)";fi
+MSGFPlusAdapter -test -ini MSGFPlusAdapter_1.ini -database proteins.fasta -in spectra.mzML -out MSGFPlusAdapter_1_out1.tmp -mzid_out MSGFPlusAdapter_1_out2.tmp.mzid -executable "${MSGFPLUS_BINARY}" > TOPP_MSGFPlusAdapter_1.stdout 2> TOPP_MSGFPlusAdapter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MSGFPlusAdapter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MSGFPlusAdapter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MSGFPlusAdapter_1.stdout)";fi
+CruxAdapter -test -ini CruxAdapter_1.ini -database proteins.fasta -in spectra_comet.mzML -out CruxAdapter_1_out1.tmp -crux_executable "${CRUX_BINARY}" -run_percolator false -decoy-format peptide-reverse > TOPP_CruxAdapter_1.stdout 2> TOPP_CruxAdapter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_CruxAdapter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_CruxAdapter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_CruxAdapter_1.stdout)";fi
+CometAdapter -test -ini CometAdapter_1.ini -database proteins.fasta -in spectra_comet.mzML -out CometAdapter_1_out1.tmp -pin_out CometAdapter_1_out2.tmp.tsv -comet_executable "${COMET_BINARY}" > TOPP_CometAdapter_1.stdout 2> TOPP_CometAdapter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_CometAdapter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_CometAdapter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_CometAdapter_1.stdout)";fi
+FileConverter -test -in CometAdapter_2_in.mzML -out CometAdapter_2_prepared.mzML -force_TPP_compatibility > TOPP_CometAdapter_2_prepare.stdout 2> TOPP_CometAdapter_2_prepare.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_CometAdapter_2_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_CometAdapter_2_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_CometAdapter_2_prepare.stdout)";fi
+CometAdapter -test -database CometAdapter_2_in.fasta -in CometAdapter_2_prepared.mzML -out CometAdapter_2_out1.tmp -pin_out CometAdapter_2_out2.tmp.tsv -comet_executable "${COMET_BINARY}" -precursor_mass_tolerance 3 -precursor_error_units Da -ini CometAdapter_1.ini > TOPP_CometAdapter_2.stdout 2> TOPP_CometAdapter_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_CometAdapter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_CometAdapter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_CometAdapter_2.stdout)";fi
+CometAdapter -test -ini CometAdapter_3.ini -database CometAdapter_3.fasta -in CometAdapter_3.mzML -out CometAdapter_3_out1.tmp -pin_out CometAdapter_3_out2.tmp.tsv -comet_executable "${COMET_BINARY}" > TOPP_CometAdapter_3.stdout 2> TOPP_CometAdapter_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_CometAdapter_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_CometAdapter_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_CometAdapter_3.stdout)";fi
+MaRaClusterAdapter -test -ini MaRaClusterAdapter_1.ini -in MaRaClusterAdapter_1_in_1.mzML MaRaClusterAdapter_1_in_2.mzML -consensus_out MaRaClusterAdapter_1_out_1.tmp.mzML -maracluster_executable "${MARACLUSTER_BINARY}" > TOPP_MaRaClusterAdapter_1.stdout 2> TOPP_MaRaClusterAdapter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MaRaClusterAdapter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MaRaClusterAdapter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MaRaClusterAdapter_1.stdout)";fi
+MaRaClusterAdapter -test -ini MaRaClusterAdapter_2.ini -in MaRaClusterAdapter_1_in_1.mzML MaRaClusterAdapter_1_in_2.mzML -id_in MaRaClusterAdapter_1_in_3.idXML -out MaRaClusterAdapter_2_out_1.tmp.idXML -maracluster_executable "${MARACLUSTER_BINARY}" > TOPP_MaRaClusterAdapter_2.stdout 2> TOPP_MaRaClusterAdapter_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MaRaClusterAdapter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MaRaClusterAdapter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MaRaClusterAdapter_2.stdout)";fi
+PercolatorAdapter -test -ini PercolatorAdapter_1.ini -in PercolatorAdapter_1.idXML -out PercolatorAdapter_1_out1.tmp -out_type idXML -percolator_executable "${PERCOLATOR_BINARY}" > TOPP_PercolatorAdapter_1.stdout 2> TOPP_PercolatorAdapter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PercolatorAdapter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PercolatorAdapter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PercolatorAdapter_1.stdout)";fi
+PercolatorAdapter -test -osw_level ms1 -in_osw PercolatorAdapter_2.osw -out PercolatorAdapter_2_out1.osw -out_type osw -percolator_executable "${PERCOLATOR_BINARY}" > TOPP_PercolatorAdapter_2.stdout 2> TOPP_PercolatorAdapter_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PercolatorAdapter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PercolatorAdapter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PercolatorAdapter_2.stdout)";fi
+PercolatorAdapter -test -osw_level ms2 -in_osw PercolatorAdapter_2_out1.osw -out PercolatorAdapter_3_out1.osw -out_type osw -percolator_executable "${PERCOLATOR_BINARY}" > TOPP_PercolatorAdapter_3.stdout 2> TOPP_PercolatorAdapter_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PercolatorAdapter_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PercolatorAdapter_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PercolatorAdapter_3.stdout)";fi
+PercolatorAdapter -test -osw_level transition -in_osw PercolatorAdapter_3_out1.osw -out PercolatorAdapter_4_out1.osw -out_type osw -percolator_executable "${PERCOLATOR_BINARY}" > TOPP_PercolatorAdapter_4.stdout 2> TOPP_PercolatorAdapter_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PercolatorAdapter_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PercolatorAdapter_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PercolatorAdapter_4.stdout)";fi
+PercolatorAdapter -test -ini PercolatorAdapter_1.ini -in PercolatorAdapter_1.idXML -out PercolatorAdapter_1_out1.tmp -out_type idXML -percolator_executable "${PERCOLATOR_BINARY}" -out_pin PercolatorAdapter_1_out1.tsv > TOPP_PercolatorAdapter_5.stdout 2> TOPP_PercolatorAdapter_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_PercolatorAdapter_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_PercolatorAdapter_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_PercolatorAdapter_5.stdout)";fi
+MascotAdapterOnline -test -ini MascotAdapterOnline_1.ini -Mascot_parameters:database SwissProt -in spectra_comet.mzML -out MascotAdapterOnline_1_out1.tmp > TOPP_MascotAdapterOnline_1.stdout 2> TOPP_MascotAdapterOnline_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MascotAdapterOnline_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MascotAdapterOnline_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MascotAdapterOnline_1.stdout)";fi
+FidoAdapter -test -in FidoAdapter_1_input.idXML -out FidoAdapter_1_output.tmp -fidocp_executable "${FIDOCHOOSEPARAMS_BINARY}" > TOPP_FidoAdapter_1.stdout 2> TOPP_FidoAdapter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FidoAdapter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FidoAdapter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FidoAdapter_1.stdout)";fi
+FidoAdapter -test -in FidoAdapter_1_input.idXML -out FidoAdapter_2_output.tmp -fidocp_executable "${FIDOCHOOSEPARAMS_BINARY}" -separate_runs > TOPP_FidoAdapter_2.stdout 2> TOPP_FidoAdapter_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FidoAdapter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FidoAdapter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FidoAdapter_2.stdout)";fi
+FidoAdapter -test -in FidoAdapter_1_input.idXML -out FidoAdapter_3_output.tmp -fidocp_executable "${FIDOCHOOSEPARAMS_BINARY}" -group_level -all_PSMs > TOPP_FidoAdapter_3.stdout 2> TOPP_FidoAdapter_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FidoAdapter_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FidoAdapter_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FidoAdapter_3.stdout)";fi
+FidoAdapter -test -in FidoAdapter_4_input.idXML -out FidoAdapter_4_output.tmp -fidocp_executable "${FIDOCHOOSEPARAMS_BINARY}" > TOPP_FidoAdapter_4.stdout 2> TOPP_FidoAdapter_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FidoAdapter_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FidoAdapter_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FidoAdapter_4.stdout)";fi
+FidoAdapter -test -greedy_group_resolution -in FidoAdapter_5_input.idXML -out FidoAdapter_5_output.tmp -fidocp_executable "${FIDOCHOOSEPARAMS_BINARY}" > TOPP_FidoAdapter_5.stdout 2> TOPP_FidoAdapter_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FidoAdapter_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FidoAdapter_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FidoAdapter_5.stdout)";fi
+FidoAdapter -test -in FidoAdapter_1_input.idXML -out FidoAdapter_6_output.tmp -fido_executable "${FIDO_BINARY}" -prob:protein 0.9 -prob:peptide 0.01 -prob:spurious 0.0 > TOPP_FidoAdapter_6.stdout 2> TOPP_FidoAdapter_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_FidoAdapter_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_FidoAdapter_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_FidoAdapter_6.stdout)";fi
+MSFraggerAdapter -test -java_heapmemory 2600 -in spectra.mzML -executable "${MSFRAGGER_BINARY}" -database proteins.fasta -out MSFraggerAdapter_7_out_tmp.idXML -opt_out MSFraggerAdapter_7_opt_out_tmp.pepXML -varmod:enable_common -digest:num_enzyme_termini semi > TOPP_MSFraggerAdapter_7.stdout 2> TOPP_MSFraggerAdapter_7.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MSFraggerAdapter_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MSFraggerAdapter_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MSFraggerAdapter_7.stdout)";fi
+MSFraggerAdapter -test -java_heapmemory 2600 -in spectra_comet.mzML -executable "${MSFRAGGER_BINARY}" -database proteins.fasta -out MSFraggerAdapter_8_out_tmp.idXML -varmod:enable_common -digest:num_enzyme_termini semi > TOPP_MSFraggerAdapter_8.stdout 2> TOPP_MSFraggerAdapter_8.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_MSFraggerAdapter_8 failed'; >&2 echo -e "stderr:\n$(cat TOPP_MSFraggerAdapter_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_MSFraggerAdapter_8.stdout)";fi
+FileConverter -test -in ginkgotoxin-ms-switching.raw -ThermoRaw_executable "${THERMORAWFILEPARSER_BINARY}" -out ginkgotoxin-ms-switching_out_tmp.mzML > TOPP_THERMORAWFILEPARSER_1.stdout 2> TOPP_THERMORAWFILEPARSER_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_THERMORAWFILEPARSER_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_THERMORAWFILEPARSER_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_THERMORAWFILEPARSER_1.stdout)";fi
+SiriusAdapter -test -executable "${SIRIUS_BINARY}" -in SiriusAdapter_1_input.mzML -out_sirius SiriusAdapter_1_output.tmp -sirius:auto_charge -sirius:profile qtof -sirius:database all -sirius:cores 1 > TOPP_SiriusAdapter_1.stdout 2> TOPP_SiriusAdapter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SiriusAdapter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SiriusAdapter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SiriusAdapter_1.stdout)";fi
+SiriusAdapter -test -executable "${SIRIUS_BINARY}" -in SiriusAdapter_2_input.mzML -in_featureinfo SiriusAdapter_2_input.featureXML -out_sirius SiriusAdapter_2_output.tmp -preprocessing:feature_only -preprocessing:filter_by_num_masstraces 3 -sirius:auto_charge -sirius:profile qtof -sirius:database all -sirius:cores 1 > TOPP_SiriusAdapter_2.stdout 2> TOPP_SiriusAdapter_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SiriusAdapter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SiriusAdapter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SiriusAdapter_2.stdout)";fi
+SiriusAdapter -test -executable "${SIRIUS_BINARY}" -in SiriusAdapter_3_input.mzML -in_featureinfo SiriusAdapter_3_input.featureXML -out_sirius SiriusAdapter_3_output.tmp -preprocessing:filter_by_num_masstraces 3 -sirius:auto_charge -sirius:profile qtof -sirius:database all -sirius:cores 1 > TOPP_SiriusAdapter_3.stdout 2> TOPP_SiriusAdapter_3.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SiriusAdapter_3 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SiriusAdapter_3.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SiriusAdapter_3.stdout)";fi
+SiriusAdapter -test -executable "${SIRIUS_BINARY}" -in SiriusAdapter_3_input.mzML -in_featureinfo SiriusAdapter_3_input.featureXML -out_ms SiriusAdapter_5_output.tmp -converter_mode > TOPP_SiriusAdapter_5.stdout 2> TOPP_SiriusAdapter_5.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SiriusAdapter_5 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SiriusAdapter_5.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SiriusAdapter_5.stdout)";fi
+SiriusAdapter -test -executable "${SIRIUS_BINARY}" -in SiriusAdapter_4_input.mzML -in_featureinfo SiriusAdapter_4_input.featureXML -out_ms SiriusAdapter_6_output.tmp -converter_mode > TOPP_SiriusAdapter_6.stdout 2> TOPP_SiriusAdapter_6.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SiriusAdapter_6 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SiriusAdapter_6.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SiriusAdapter_6.stdout)";fi
+SiriusAdapter -test -executable "${SIRIUS_BINARY}" -in SiriusAdapter_4_input.mzML -in_featureinfo SiriusAdapter_4_input.featureXML -out_sirius SiriusAdapter_7_output.tmp -preprocessing:feature_only -sirius:profile qtof -sirius:database all -sirius:cores 1 > TOPP_SiriusAdapter_7.stdout 2> TOPP_SiriusAdapter_7.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SiriusAdapter_7 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SiriusAdapter_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SiriusAdapter_7.stdout)";fi
+AssayGeneratorMetabo -test -executable "${SIRIUS_BINARY}" -in AssayGeneratorMetabo_input.mzML -in_id AssayGeneratorMetabo_ams_input.featureXML -out AssayGeneratorMetabo_ams_sirius_output.tmp.tsv -fragment_annotation sirius -use_exact_mass -transition_threshold 3.0 -min_transitions 2 -max_transitions 3 -preprocessing:filter_by_num_masstraces 1 -preprocessing:precursor_mz_tolerance 10 -preprocessing:precursor_mz_tolerance_unit ppm -preprocessing:feature_only -sirius:profile qtof -sirius:compound_timeout 100 > UTILS_AssayGeneratorMetabo_7.stdout 2> UTILS_AssayGeneratorMetabo_7.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AssayGeneratorMetabo_7 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AssayGeneratorMetabo_7.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AssayGeneratorMetabo_7.stdout)";fi
+AssayGeneratorMetabo -test -executable "${SIRIUS_BINARY}" -in AssayGeneratorMetabo_input.mzML -in_id AssayGeneratorMetabo_ams_input.featureXML -out AssayGeneratorMetabo_ams_sirius_ukn_output.tmp.tsv -fragment_annotation sirius -use_exact_mass -transition_threshold 3.0 -min_transitions 2 -max_transitions 3 -preprocessing:filter_by_num_masstraces 1 -preprocessing:precursor_mz_tolerance 10 -preprocessing:precursor_mz_tolerance_unit ppm -preprocessing:feature_only -sirius:profile qtof -sirius:compound_timeout 100 -use_known_unknowns > UTILS_AssayGeneratorMetabo_8.stdout 2> UTILS_AssayGeneratorMetabo_8.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AssayGeneratorMetabo_8 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AssayGeneratorMetabo_8.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AssayGeneratorMetabo_8.stdout)";fi
+AssayGeneratorMetabo -test -executable "${SIRIUS_BINARY}" -in AssayGeneratorMetabo_intsort_input.mzML -in_id AssayGeneratorMetabo_intsort_input.featureXML -out AssayGeneratorMetabo_ams_sirius_intsort_output.tmp.tsv -fragment_annotation sirius -use_exact_mass -transition_threshold 3.0 -min_transitions 2 -max_transitions 3 -preprocessing:filter_by_num_masstraces 1 -preprocessing:precursor_mz_tolerance 10 -preprocessing:precursor_mz_tolerance_unit ppm -preprocessing:feature_only -sirius:profile qtof -sirius:compound_timeout 100 > UTILS_AssayGeneratorMetabo_9.stdout 2> UTILS_AssayGeneratorMetabo_9.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AssayGeneratorMetabo_9 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AssayGeneratorMetabo_9.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AssayGeneratorMetabo_9.stdout)";fi
+AssayGeneratorMetabo -test -executable "${SIRIUS_BINARY}" -in AssayGeneratorMetabo_input.mzML -in_id AssayGeneratorMetabo_ams_input.featureXML -out AssayGeneratorMetabo_ams_sirius_restrict_output.tmp.tsv -fragment_annotation sirius -use_exact_mass -transition_threshold 3.0 -min_transitions 2 -max_transitions 3 -min_fragment_mz 100 -max_fragment_mz 900 -preprocessing:filter_by_num_masstraces 1 -preprocessing:precursor_mz_tolerance 10 -preprocessing:precursor_mz_tolerance_unit ppm -preprocessing:feature_only -sirius:profile qtof -sirius:compound_timeout 100 > UTILS_AssayGeneratorMetabo_10.stdout 2> UTILS_AssayGeneratorMetabo_10.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'UTILS_AssayGeneratorMetabo_10 failed'; >&2 echo -e "stderr:\n$(cat UTILS_AssayGeneratorMetabo_10.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat UTILS_AssayGeneratorMetabo_10.stdout)";fi
+SiriusAdapter -test -executable "${SIRIUS_BINARY}" -in SiriusAdapter_2_input.mzML -in_featureinfo SiriusAdapter_2_input.featureXML -out_sirius SiriusAdapter_4_output.tmp -out_fingerid SiriusAdapter_4_foutput.tmp -sirius:auto_charge -sirius:profile qtof -sirius:database all > TOPP_SiriusAdapter_4.stdout 2> TOPP_SiriusAdapter_4.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SiriusAdapter_4 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SiriusAdapter_4.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SiriusAdapter_4.stdout)";fi
+NovorAdapter -test -java_memory 512 -executable "${NOVOR_BINARY}" -in NovorAdapter_in.mzML -out NovorAdapter_1_out.tmp -variable_modifications "Acetyl (K)" -fixed_modifications "Carbamidomethyl (C)" -forbiddenResidues "I" > TOPP_NovorAdapter_1.stdout 2> TOPP_NovorAdapter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_NovorAdapter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_NovorAdapter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_NovorAdapter_1.stdout)";fi
+FileConverter -test -force_TPP_compatibility -in spectra_spectrast.mzXML -out SpectrastAdapter_1_hack.mzML > TOPP_SpectrastSearchAdapter_0_prepare.stdout 2> TOPP_SpectrastSearchAdapter_0_prepare.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SpectrastSearchAdapter_0_prepare failed'; >&2 echo -e "stderr:\n$(cat TOPP_SpectrastSearchAdapter_0_prepare.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SpectrastSearchAdapter_0_prepare.stdout)";fi
+SpectraSTSearchAdapter -test -library_file testLib.splib -spectra_files SpectrastAdapter_1_hack.mzML -output_files SpectrastAdapter_1_out1.tmp.pep.xml -executable "${SPECTRAST_BINARY}" > TOPP_SpectrastSearchAdapter_1.stdout 2> TOPP_SpectrastSearchAdapter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SpectrastSearchAdapter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SpectrastSearchAdapter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SpectrastSearchAdapter_1.stdout)";fi
+SpectraSTSearchAdapter -test -library_file testLib.splib -spectra_files SpectrastAdapter_1_hack.mzML -output_files SpectrastAdapter_1_out1.tmp.pep.tsv -executable "${SPECTRAST_BINARY}" > TOPP_SpectrastSearchAdapter_2.stdout 2> TOPP_SpectrastSearchAdapter_2.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_SpectrastSearchAdapter_2 failed'; >&2 echo -e "stderr:\n$(cat TOPP_SpectrastSearchAdapter_2.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_SpectrastSearchAdapter_2.stdout)";fi
+LuciphorAdapter -test -in LuciphorAdapter_1_input.mzML -java_memory 1024 -id LuciphorAdapter_1_input.idXML -out LuciphorAdapter_1_output.tmp -executable "${LUCIPHOR_BINARY}" -min_num_psms_model 1 > TOPP_LuciphorAdapter_1.stdout 2> TOPP_LuciphorAdapter_1.stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'TOPP_LuciphorAdapter_1 failed'; >&2 echo -e "stderr:\n$(cat TOPP_LuciphorAdapter_1.stderr | sed 's/^/ /')"; echo -e "stdout:\n$(cat TOPP_LuciphorAdapter_1.stdout)";fi
diff -r 000000000000 -r 8fad84d1a74d prepare_test_data_manual.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/prepare_test_data_manual.sh Wed Sep 09 20:04:20 2020 +0000
@@ -0,0 +1,155 @@
+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
+
+# TODO OpenSwathDIAPreScoring
+
+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
+
+# TODO out should be tsv, but needs https://github.com/OpenMS/OpenMS/pull/4533
+RTEvaluation -in PeptideIndexer_1.idXML -out RTEvaluation.csv > RTEvaluation.stdout 2> stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'RTEvaluation failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi
+ln -fs RTEvaluation.csv RTEvaluation.tsv > .stdout 2> stderr
+
+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
diff -r 000000000000 -r 8fad84d1a74d readme.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.md Wed Sep 09 20:04:20 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.
+
diff -r 000000000000 -r 8fad84d1a74d test-data.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data.sh Wed Sep 09 20:04:20 2020 +0000
@@ -0,0 +1,255 @@
+#!/usr/bin/env bash
+
+VERSION=2.5
+FILETYPES="filetypes.txt"
+CONDAPKG="https://anaconda.org/bioconda/openms/2.5.0/download/linux-64/openms-2.5.0-h463af6b_1.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 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)"
+
+if [[ -z "$1" ]]; then
+ autotests="/dev/null"
+else
+ autotests="$1"
+fi
+
+###############################################################################
+## 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 openjdk=8.0.192 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 $CTDCONVERTER
+ git pull origin topic/cdata
+ cd -
+fi
+export PYTHONPATH=$(pwd)/CTDopts
+
+###############################################################################
+## 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"
+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 -q 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
+ wget http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip
+ unzip -e PepNovo.20120423.zip -d /tmp/
+ mv /tmp/Models test-data/pepnovo_models/
+fi
+###############################################################################
+## generate ctd files using the binaries in the conda package
+###############################################################################
+echo "Create CTD files"
+conda activate $OPENMSENV
+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="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
+
+
+# # # exit
+
+###############################################################################
+## auto generate tests
+###############################################################################
+
+echo "Write test macros to "$autotests
+echo "" > $autotests
+for i in $(ls *xml |grep -v macros)
+do
+ b=$(basename "$i" .xml)
+ get_tests2 "$b" >> $autotests
+done
+echo "" >> $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
+if [[ ! -z "$1" ]]; then
+ echo "" > macros_discarded_auto.xml
+ for i in OpenSwathFileSplitter IDRipper MzMLSplitter
+ do
+ echo "" >> macros_discarded_auto.xml
+ xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >> macros_discarded_auto.xml
+ echo "" >> macros_discarded_auto.xml
+ xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp
+ mv tmp macros_autotest.xml
+ done
+ >&2 "discarded autogenerated macros for curation in macros_discarded_auto.xml"
+fi
+conda deactivate
+
+## remove broken symlinks in test-data
+find test-data/ -xtype l -delete
+
+# if [ ! -z "$created" ]; then
+# echo "Removing temporary directory"
+# rm -rf "$tmp"
+# fi
diff -r 000000000000 -r 8fad84d1a74d tool-data/pepnovo_models.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/pepnovo_models.loc.sample Wed Sep 09 20:04:20 2020 +0000
@@ -0,0 +1,23 @@
+# This is a sample file distributed with Galaxy that enables tools
+# to use pepnovo models
+# The file has three tab separated columns: name, value, and path.
+# The idea is that there are a number of models in a directory:
+# - each model directory has a unique name (columns 2 and 0)
+# - each model can contain a set of models (column 1)
+#
+# The following example works fo the default models from
+# http://proteomics.ucsd.edu/Software/PepNovo.html (just remove the comment
+# chars and replace DIR_TO_PEPNOVO_MODELS)
+
+#default_models CID_IT_TRYP DIR_TO_PEPNOVO_MODELS
+#default_models LTQ_COMP DIR_TO_PEPNOVO_MODELS
+#default_models DBC4_PEAK DIR_TO_PEPNOVO_MODELS
+#default_models CID_IT_TRYP_TAG5 DIR_TO_PEPNOVO_MODELS
+#default_models CID_IT_TRYP_TAG6 DIR_TO_PEPNOVO_MODELS
+#default_models ITDNV_PEAK DIR_TO_PEPNOVO_MODELS
+#default_models CID_IT_TRYP_SCORE DIR_TO_PEPNOVO_MODELS
+#default_models CID_IT_TRYP_TAG3 DIR_TO_PEPNOVO_MODELS
+#default_models CID_IT_TRYP_DNVPART DIR_TO_PEPNOVO_MODELS
+#default_models CID_IT_TRYP_TAG4 DIR_TO_PEPNOVO_MODELS
+#default_models CID_IT_TRYP_DB DIR_TO_PEPNOVO_MODELS
+#default_models CID_IT_TRYP_CSP DIR_TO_PEPNOVO_MODELS
diff -r 000000000000 -r 8fad84d1a74d tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Wed Sep 09 20:04:20 2020 +0000
@@ -0,0 +1,7 @@
+
+
+
+
diff -r 000000000000 -r 8fad84d1a74d tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Wed Sep 09 20:04:20 2020 +0000
@@ -0,0 +1,7 @@
+
+
+
+
diff -r 000000000000 -r 8fad84d1a74d tools_blacklist.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools_blacklist.txt Wed Sep 09 20:04:20 2020 +0000
@@ -0,0 +1,24 @@
+# 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
+
+# seems currently unusable https://github.com/OpenMS/OpenMS/pull/4443
+OpenSwathDIAPreScoring
+
+# https://github.com/OpenMS/OpenMS/issues/4550#issuecomment-594065727
+ProteomicsLFQ
+
+# https://github.com/OpenMS/OpenMS/issues/4401
+InclusionExclusionListCreator
+RTPredict
+PTPredict