# HG changeset patch
# User galaxyp
# Date 1602619084 0
# Node ID 5aabc469cce09c5635e2660a8d377154690a940a
# Parent  24a506151bdf627a4449f18c8c4c9eb4ba1b6173
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"

diff -r 24a506151bdf -r 5aabc469cce0 404-urls.patch
--- a/404-urls.patch	Thu Sep 24 09:54:05 2020 +0000
+++ b/404-urls.patch	Tue Oct 13 19:58:04 2020 +0000
@@ -1,65 +1,11 @@
-diff -ruN ClusterMassTracesByPrecursor.xml ClusterMassTracesByPrecursor.xml
---- ClusterMassTracesByPrecursor.xml	2020-09-21 17:02:36.060104555 +0200
-+++ ClusterMassTracesByPrecursor.xml	2020-09-21 17:00:02.864815223 +0200
-@@ -75,8 +75,6 @@
-     <expand macro="manutest_ClusterMassTracesByPrecursor"/>
-   </tests>
-   <help><![CDATA[Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile.
--
--
--For more information, visit http://www.openms.de/documentation/UTILS_ClusterMassTracesByPrecursor.html]]></help>
-+]]></help>
-   <expand macro="references"/>
- </tool>
-diff -ruN ClusterMassTraces.xml ClusterMassTraces.xml
---- ClusterMassTraces.xml	2020-09-21 17:02:36.060104555 +0200
-+++ ClusterMassTraces.xml	2020-09-21 17:00:22.192722036 +0200
-@@ -69,8 +69,6 @@
-     <expand macro="manutest_ClusterMassTraces"/>
-   </tests>
-   <help><![CDATA[Creates pseudo spectra.
--
--
--For more information, visit http://www.openms.de/documentation/UTILS_ClusterMassTraces.html]]></help>
-+]]></help>
+diff -ruN FeatureFinderSuperHirn.xml FeatureFinderSuperHirn.xml
+--- FeatureFinderSuperHirn.xml	2020-10-02 12:06:56.398572301 +0200
++++ FeatureFinderSuperHirn.xml	2020-10-02 12:07:31.511153834 +0200
+@@ -105,6 +105,6 @@
+   <help><![CDATA[Finds mass spectrometric features in mass spectra.
+ 
+ 
+-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureFinderSuperHirn.html]]></help>
++For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.6.0/html/UTILS_FeatureFinderSuperHirn.html]]></help>
    <expand macro="references"/>
  </tool>
-diff -ruN FeatureFinderSuperHirn.xml FeatureFinderSuperHirn.xml
---- FeatureFinderSuperHirn.xml	2020-09-21 17:02:36.060104555 +0200
-+++ FeatureFinderSuperHirn.xml	2020-09-21 17:00:42.372625907 +0200
-@@ -103,8 +103,6 @@
-     <expand macro="manutest_FeatureFinderSuperHirn"/>
-   </tests>
-   <help><![CDATA[Finds mass spectrometric features in mass spectra.
--
--
--For more information, visit http://www.openms.de/documentation/TOPP_FeatureFinderSuperHirn.html]]></help>
-+]]></help>
-   <expand macro="references"/>
- </tool>
-diff -ruN MSFraggerAdapter.xml MSFraggerAdapter.xml
---- MSFraggerAdapter.xml	2020-09-21 17:02:36.060104555 +0200
-+++ MSFraggerAdapter.xml	2020-09-21 17:01:04.892519985 +0200
-@@ -250,8 +250,6 @@
-     <expand macro="manutest_MSFraggerAdapter"/>
-   </tests>
-   <help><![CDATA[Peptide Identification with MSFragger
--
--
--For more information, visit http://www.openms.de/documentation/UTILS_MSFraggerAdapter.html]]></help>
-+]]></help>
-   <expand macro="references"/>
- </tool>
-diff -ruN SimpleSearchEngine.xml SimpleSearchEngine.xml
---- SimpleSearchEngine.xml	2020-09-21 17:02:36.060104555 +0200
-+++ SimpleSearchEngine.xml	2020-09-21 17:01:33.020389600 +0200
-@@ -5373,8 +5373,6 @@
-     <expand macro="manutest_SimpleSearchEngine"/>
-   </tests>
-   <help><![CDATA[Annotates MS/MS spectra using SimpleSearchEngine.
--
--
--For more information, visit http://www.openms.de/documentation/UTILS_SimpleSearchEngine.html]]></help>
-+]]></help>
-   <expand macro="references"/>
- </tool>
diff -r 24a506151bdf -r 5aabc469cce0 MzMLSplitter.xml
--- a/MzMLSplitter.xml	Thu Sep 24 09:54:05 2020 +0000
+++ b/MzMLSplitter.xml	Tue Oct 13 19:58:04 2020 +0000
@@ -52,12 +52,12 @@
     <param name="no_chrom" argument="-no_chrom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove chromatograms, keep only spectra" help=""/>
     <param name="no_spec" argument="-no_spec" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove spectra, keep only chromatograms" help=""/>
     <expand macro="adv_opts_macro">
-      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
+      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
       <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
         <expand macro="list_string_san"/>
       </param>
     </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
@@ -76,6 +76,6 @@
   <help><![CDATA[Splits an mzML file into multiple parts
 
 
-For more information, visit http://www.openms.de/documentation/UTILS_MzMLSplitter.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MzMLSplitter.html]]></help>
   <expand macro="references"/>
 </tool>
diff -r 24a506151bdf -r 5aabc469cce0 filetypes.txt
--- a/filetypes.txt	Thu Sep 24 09:54:05 2020 +0000
+++ b/filetypes.txt	Tue Oct 13 19:58:04 2020 +0000
@@ -53,7 +53,7 @@
 paramXML      paramxml
 fasta         peff
 peplist       peplist
-# TODO pep.xml should be removed with OMS 2.6 https://github.com/OpenMS/OpenMS/pull/4541
+# TODO pep.xml should be removed with OMS 2.6 https://github.com/OpenMS/OpenMS/pull/4541 .. but still in the tests
 pep.xml       pepxml
 pepXML        pepxml
 png           png
diff -r 24a506151bdf -r 5aabc469cce0 generate-foo.sh
--- a/generate-foo.sh	Thu Sep 24 09:54:05 2020 +0000
+++ b/generate-foo.sh	Tue Oct 13 19:58:04 2020 +0000
@@ -2,125 +2,126 @@
 
 # parse test definitions from OpenMS sources for a tool with a given id
 function get_tests2 {
-	id=$1
-	>&2 echo "generate tests for $id"
-	echo '<xml name="autotest_'"$id"'">'
+    id=$1
+    >&2 echo "generate tests for $id"
+    echo '<xml name="autotest_'"$id"'">'
 
-	# 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
+    # get the tests from the CMakeLists.txt
+    # 1st remove some tests
+    # - OpenSwathMzMLFileCacher with -convert_back argumen https://github.com/OpenMS/OpenMS/issues/4399
     # - IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differentlt
-	# - several tools with duplicated input (leads to conflict when linking)
-	# - TOFCalibration inputs we extension (also in prepare_test_data) https://github.com/OpenMS/OpenMS/pull/4525
-	# - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456)
-	# - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed)
-	# - some input files are originally in a subdir (degenerated cases/), but not in test-data
-	# - SeedListGenerator: https://github.com/OpenMS/OpenMS/issues/4404
-	# - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet)
-	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/${TMP_RIP_PATH}/""/' |
-		sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @' |
-		grep -v "MaRaClusterAdapter.*-consensus_out"|
- 		grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " |
-		sed 's@degenerate_cases/@@g' |
-		grep -v 'TOPP_SeedListGenerator_3"' | 
-		egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"')
+    # - several tools with duplicated input (leads to conflict when linking)
+    # - TOFCalibration inputs we extension (also in prepare_test_data) https://github.com/OpenMS/OpenMS/pull/4525
+    # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456)
+    # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed)
+    # - some input files are originally in a subdir (degenerated cases/), but not in test-data
+    # - SeedListGenerator: https://github.com/OpenMS/OpenMS/issues/4404
+    # - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet)
+    # - FeatureFinderIdentification name clash of two tests https://github.com/OpenMS/OpenMS/pull/5002
+    # - TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010
+    CMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake  |
+        sed 's@${DATA_DIR_SHARE}/@@g' |
+        grep -v 'OpenSwathMzMLFileCacher .*-convert_back' |
+        sed 's/${TMP_RIP_PATH}/""/' |
+        grep -v "MaRaClusterAdapter.*-consensus_out"|
+        grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " |
+        sed 's@degenerate_cases/@@g' |
+        grep -v 'TOPP_SeedListGenerator_3"' | 
+        egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"' |
+	egrep -v '"TOPP_FeatureFinderIdentification_4"' | 
+	sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/')
 
 
-# 		grep -v 'FileFilter.*-spectra:select_polarity ""' |
-# 		grep -v 'MassTraceExtractor_2.ini ' |
-# 		grep -v "FileMerger_6_input2.mzML.*FileMerger_6_input2.mzML" |
-# 		grep -v "IDMerger_1_input1.idXML.*IDMerger_1_input1.idXML" |
-# 		grep -v "degenerated_empty.idXML.*degenerated_empty.idXML" |
-# 		grep -v "FeatureLinkerUnlabeledKD_1_output.consensusXML.*FeatureLinkerUnlabeledKD_1_output.consensusXML" |
-# 		grep -v "FeatureLinkerUnlabeledQT_1_output.consensusXML.*FeatureLinkerUnlabeledQT_1_output.consensusXML" |
+#         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) $line"
-			continue
-		fi
+    # 1st part is a dirty hack to join lines containing a single function call, e.g.
+    # addtest(....
+    #         ....)
+    echo "$CMAKE" | sed 's/#.*//; s/^\s*//; s/\s*$//' | grep -v "^#" | grep -v "^$"  | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | 
+        grep -iE "add_test\(\"(TOPP|UTILS)_.*/$id " | egrep -v "_prepare\"|_convert|WRITEINI|WRITECTD|INVALIDVALUE"  | while read -r line
+    do
+        line=$(echo "$line" | sed 's/add_test("\([^"]\+\)"/\1/; s/)$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g')
+        # >&2 echo $line
+        test_id=$(echo "$line" | cut -d" " -f 1)
+        tool_id=$(echo "$line" | cut -d" " -f 2)
+        if [[ $test_id =~ _out_?[0-9]? ]]; then
+            >&2 echo "    skip $test_id $line"
+            continue
+        fi
+        if [[ ${id,,} != ${tool_id,,} ]]; then
+            >&2 echo "    skip $test_id ($id != $tool_id) $line"
+            continue
+        fi
 
-		#remove tests with set_tests_properties(....PROPERTIES WILL_FAIL 1)
-		if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then
-			>&2 echo "    skip failing "$test_id
-			continue
-		fi
-		tes="  <test>\n"
-		line=$(fix_tmp_files "$line")
-		line=$(unique_files "$line")
-		# >&2 echo $line
-		#if there is an ini file then we use this to generate the test
-		#otherwise the ctd file is used
-		#other command line parameters are inserted later into this xml
-		if grep -lq "\-ini" <<<"$line"; then
-			ini=$(echo $line | sed 's/.*-ini \([^ ]\+\).*/\1/')
-			ini="test-data/$ini"
-		else
-			ini="ctd/$tool_id.ctd"
-		fi
-		cli=$(echo $line |cut -d" " -f3- | sed 's/-ini [^ ]\+//')
-		
-		ctdtmp=$(mktemp)
-		#echo python3 fill_ctd_clargs.py --ctd $ini $cli
-		# using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"])
-		# >&2 echo "python3 fill_ctd_clargs.py --ctd $ini $cli"
-		eval "python3 fill_ctd_clargs.py --ctd $ini $cli" > "$ctdtmp"
-		# echo $ctdtmp
- 		# >&2 cat $ctdtmp
-  		testtmp=$(mktemp)
- 		python3 $CTDCONVERTER/convert.py galaxy -i $ctdtmp -o $testtmp -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf  -p hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib > /dev/null
-	   	cat $testtmp | grep -v '<output.*file=""' # | grep -v 'CHEMISTRY/'
-		rm $ctdtmp $testtmp
+        #remove tests with set_tests_properties(....PROPERTIES WILL_FAIL 1)
+        if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then
+            >&2 echo "    skip failing "$test_id
+            continue
+        fi
+        tes="  <test>\n"
+        line=$(fix_tmp_files "$line")
+        line=$(unique_files "$line")
+        # >&2 echo $line
+        #if there is an ini file then we use this to generate the test
+        #otherwise the ctd file is used
+        #other command line parameters are inserted later into this xml
+        if grep -lq "\-ini" <<<"$line"; then
+            ini=$(echo $line | sed 's/.*-ini \([^ ]\+\).*/\1/')
+            ini="test-data/$ini"
+        else
+            ini="ctd/$tool_id.ctd"
+        fi
+        cli=$(echo $line |cut -d" " -f3- | sed 's/-ini [^ ]\+//')
 
-		#> /dev/null
+        ctdtmp=$(mktemp)
+        #echo python3 fill_ctd_clargs.py --ctd $ini $cli
+        # using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"])
+        # >&2 echo "python3 fill_ctd_clargs.py --ctd $ini $cli"
+        eval "python3 fill_ctd_clargs.py --ctd $ini $cli" > "$ctdtmp"
+        # echo $ctdtmp
+        # >&2 cat $ctdtmp
+        testtmp=$(mktemp)
+        python3 $CTDCONVERTER/convert.py galaxy -i $ctdtmp -o $testtmp -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf  -p hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib > /dev/null
+        cat $testtmp | grep -v '<output.*file=""' # | grep -v 'CHEMISTRY/'
+        rm $ctdtmp $testtmp
 
-		#rm $testtmp
-	done 
-	echo '</xml>'
+        #> /dev/null
+
+        #rm $testtmp
+    done 
+    echo '</xml>'
 }
 
 #some tests use the same file twice which does not work in planemo tests
 #hence we create symlinks for each file used twice
 function unique_files {
-	line=$@
-	for arg in $@
-	do
-		if [[ ! -f "test-data/$arg" ]]; then
-			continue
-		fi
-		cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n'))
-		while [[ $cnt -gt 1 ]]; do
+    line=$@
+    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
+            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
+    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}'
+    grep "^$1" "$2" | awk '{print $2}'
 }
 
 #OpenMS tests output to tmp files and compare with FuzzyDiff to the expected file.
@@ -129,34 +130,34 @@
 #(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"
+#    >&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 {
@@ -190,28 +191,32 @@
 
 # parse data preparation calls from OpenMS sources for a tool with a given id
 function prepare_test_data {
-# 	id=$1
+#     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
+# TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010
+    cat $OPENMSGIT/src/tests/topp/CMakeLists.txt  $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's/#.*$//'| sed 's/^\s*//; s/\s*$//' | grep -v "^$"  | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | 
+        sed 's/degenerate_cases\///' | 
+        egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | 
+        grep add_test | 
+        egrep "TOPP|UTILS" |
+        sed 's@${DATA_DIR_SHARE}/@@g;'|
+        sed 's@${TMP_RIP_PATH}@dummy2.tmp@g'|
+        sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'| 
+	sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' |
+    while read line
+    do
+        test_id=$(echo "$line" | sed 's/add_test(//; s/"//g;  s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f1)
 
-		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 $test_id.stdout)\";fi"	
+        if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then
+            >&2 echo "    skip failing "$test_id
+            continue
+        fi
+
+        line=$(echo "$line" | sed 's/add_test("//; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f2-)
+        # line="$(fix_tmp_files $line)"
+        echo 'echo executing "'$test_id'"'
+	echo "$line > $test_id.stdout 2> $test_id.stderr"
+        echo "if [[ \"\$?\" -ne \"0\" ]]; then >&2 echo '$test_id failed'; >&2 echo -e \"stderr:\n\$(cat $test_id.stderr | sed 's/^/    /')\"; echo -e \"stdout:\n\$(cat $test_id.stdout)\";fi"    
     done
 }
diff -r 24a506151bdf -r 5aabc469cce0 generate.sh
--- a/generate.sh	Thu Sep 24 09:54:05 2020 +0000
+++ b/generate.sh	Tue Oct 13 19:58:04 2020 +0000
@@ -1,20 +1,13 @@
 #!/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
+VERSION=2.6
 FILETYPES="filetypes.txt"
 PROFILE="20.05"
 ## FILETYPES_RE=$(grep -v "^#" $FILETYPES | grep -v "^$" | cut -f 1 -d" " | tr '\n' '|' | sed 's/|$//'| sed 's/|/\\|/g')
 
 export tmp=$(mktemp -d)
-
 export CTDCONVERTER="$tmp/CTDConverter"
 
-export PYTHONPATH="$(pwd)/CTDopts/"
 ###############################################################################
 ## reset old data
 ###############################################################################
@@ -59,6 +52,8 @@
 ###############################################################################
 ## conversion ctd->xml 
 ###############################################################################
+
+find . -maxdepth 0 -name "[A-Z]*xml" -delete
 source $(dirname $(which conda))/../etc/profile.d/conda.sh
 conda activate $tmp/OpenMS$VERSION-env
 python $CTDCONVERTER/convert.py galaxy -i ctd/*ctd -o ./ -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf  -p hardcoded_params.json --test-macros macros_autotest.xml --test-macros-prefix autotest_  --test-macros macros_test.xml --test-macros-prefix manutest_ --tool-version $VERSION --tool-profile $PROFILE > convert.out 2> convert.err
@@ -67,6 +62,10 @@
 
 patch PepNovoAdapter.xml < PepNovoAdapter.patch
 patch OMSSAAdapter.xml < OMSSAAdapter.patch
+
+# https://github.com/OpenMS/OpenMS/pull/4984
+sed -i -e 's@http://www.openms.de/documentation/@http://www.openms.de/doxygen/release/2.6.0/html/@' ./*xml
+# https://github.com/OpenMS/OpenMS/pull/4984#issuecomment-702641976
 patch -p0 <404-urls.patch
 
 # #-b version log debug test in_type executable pepnovo_executable param_model_directory rt_concat_trafo_out param_id_pool
diff -r 24a506151bdf -r 5aabc469cce0 hardcoded_params.json
--- a/hardcoded_params.json	Thu Sep 24 09:54:05 2020 +0000
+++ b/hardcoded_params.json	Tue Oct 13 19:58:04 2020 +0000
@@ -119,6 +119,10 @@
 	"threads": [{
 		"value": "${GALAXY_SLOTS:-1}"
 	}],
+	"sirius:cores": [{
+		"value": "${GALAXY_SLOTS:-1}"
+	}],
+
 	"#": "hardcode the outer loop threads for OpenSwathWorkflow",
 	"outer_loop_threads": [{
 			"value": "1", 
@@ -128,6 +132,13 @@
 		"value": ",",
 		"tools": ["IDMassAccuracy"]
 	}],
+
+	"#": "don't alow to copy data internally to save computation time for reloading",
+	"copy_data": [{
+		"value": "false",
+		"tools": ["MapAlignerTreeGuided"]
+	}],
+
 	"#": "overwrite/add Galaxy xml attributes of some parameters (names need to start with param_)",
 
 	"#": "test is not a hardcoded value since we need to set it in the tool tests", 
@@ -146,8 +157,6 @@
 
 	"#": "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": [{
@@ -157,12 +166,6 @@
 	 	"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",
@@ -172,25 +175,8 @@
 		"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",
+	"#": "XTandem Adapter output is called .xml in OMS which is to unspecific -> use Galaxy's bioml",
 	"xml_out": [{
 		"CTD:restrictions": "bioml",
 		"tools": ["XTandemAdapter"]
@@ -199,8 +185,7 @@
 	"#": "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",
+	"#": "SeedListGenerator: remove consensusXML https://github.com/OpenMS/OpenMS/issues/4404 .. see also out parameter",
 	"in": [{
 		"CTD:restrictions": "pepXML,protXML,mascotXML,omssaXML,bioml,psms,tsv,idXML,mzid,xquest.xml",
 		"tools": ["IDFileConverter"]
@@ -211,19 +196,10 @@
 		"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": [{
@@ -231,6 +207,7 @@
 		"tools": ["IDMapper"]
 	}],
 
+	"#": "hardcoding prefix parameters which are not yet available in OMS but in CTDOpts https://github.com/OpenMS/OpenMS/pull/4527",
 	"#": "output-prefix",
 	"out_path": [{
 		"CTD:type": "output-prefix", 
@@ -244,5 +221,16 @@
 		"CTD:required": true,
 		"CTD:restrictions": "mzml",
 		"tools": ["OpenSwathFileSplitter"]
+	}],
+
+	"#": "OpenSwathDIAPreScoring: https://github.com/OpenMS/OpenMS/pull/4443",
+        "#": "SpectraSTSearchAdapter does not need xml .. redundant with pep.xml TODO check if list is up to date with each new release",
+	"output_files": [{
+		"CTD:required": true,
+		"tools": ["OpenSwathDIAPreScoring"]
+	}, {
+		"CTD:restrictions": "txt,tsv,pep.xml,pepXML,html",
+		"tools": ["SpectraSTSearchAdapter"]
+	
 	}]
 }
diff -r 24a506151bdf -r 5aabc469cce0 macros.xml
--- a/macros.xml	Thu Sep 24 09:54:05 2020 +0000
+++ b/macros.xml	Tue Oct 13 19:58:04 2020 +0000
@@ -3,7 +3,7 @@
      You can edit this file to add your own macros, if you so desire, or you can
      add additional macro files using the m/macros parameter -->
 <macros>
-  <token name="@TOOL_VERSION@">2.5</token>
+  <token name="@TOOL_VERSION@">2.6</token>
   <token name="@GALAXY_VERSION@">0</token>
   <xml name="requirements">
     <requirements>
@@ -11,7 +11,6 @@
       <requirement type="package" version="@TOOL_VERSION@">openms-thirdparty</requirement>
       <!-- makeblastdb for OMSSAAdapter -->
       <requirement type="package" version="2.9.0">blast</requirement>
-      <requirement type="package" version="8.0.192">openjdk</requirement>
       <!--<requirement type="package" version="5.0.0">tpp</requirement>-->
       <!-- for realpath (used e.g. in LuciphorAdapter) -->
 	  <!--<requirement type="package" version="8.25">coreutils</requirement>-->
diff -r 24a506151bdf -r 5aabc469cce0 macros_autotest.xml
--- a/macros_autotest.xml	Thu Sep 24 09:54:05 2020 +0000
+++ b/macros_autotest.xml	Tue Oct 13 19:58:04 2020 +0000
@@ -158,7 +158,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -228,7 +227,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -298,7 +296,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -368,7 +365,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -438,7 +434,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -508,7 +503,6 @@
         <param name="compound_timeout" value="100"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -578,7 +572,6 @@
         <param name="compound_timeout" value="100"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -648,7 +641,6 @@
         <param name="compound_timeout" value="100"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -718,7 +710,6 @@
         <param name="compound_timeout" value="100"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -760,9 +751,6 @@
     <test expect_num_outputs="3">
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
-        <param name="fragment_bin_tolerance" value="1.0005"/>
-        <param name="fragment_bin_offset" value="0.25"/>
-        <param name="instrument" value="high_res"/>
         <param name="use_A_ions" value="false"/>
         <param name="use_B_ions" value="true"/>
         <param name="use_C_ions" value="false"/>
@@ -770,6 +758,7 @@
         <param name="use_Y_ions" value="true"/>
         <param name="use_Z_ions" value="false"/>
         <param name="use_NL_ions" value="false"/>
+        <param name="second_enzyme" value=""/>
         <param name="digest_mass_range" value="600:5000"/>
         <param name="max_precursor_charge" value="5"/>
         <param name="spectrum_batch_size" value="1000"/>
@@ -781,7 +770,7 @@
         <param name="clear_mz_range" value="0:0"/>
         <param name="max_variable_mods_in_peptide" value="5"/>
         <param name="require_variable_mod" value="false"/>
-        <param name="force" value="false"/>
+        <param name="force" value="true"/>
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="spectra_comet.mzML"/>
@@ -791,9 +780,15 @@
       <param name="precursor_mass_tolerance" value="3.0"/>
       <param name="precursor_error_units" value="ppm"/>
       <param name="isotope_error" value="off"/>
+      <param name="fragment_mass_tolerance" value="0.50025"/>
+      <param name="fragment_error_units" value="Da"/>
+      <param name="fragment_bin_offset" value="0.25"/>
+      <param name="instrument" value="high_res"/>
       <param name="enzyme" value="Trypsin"/>
       <param name="num_enzyme_termini" value="fully"/>
-      <param name="allowed_missed_cleavages" value="1"/>
+      <param name="missed_cleavages" value="1"/>
+      <param name="min_peptide_length" value="5"/>
+      <param name="max_peptide_length" value="63"/>
       <param name="num_hits" value="5"/>
       <param name="precursor_charge" value="0:0"/>
       <param name="override_charge" value="keep any known"/>
@@ -803,6 +798,7 @@
       <param name="clip_nterm_methionine" value="false"/>
       <param name="fixed_modifications" value=""/>
       <param name="variable_modifications" value=""/>
+      <param name="binary_modifications" value=""/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
@@ -813,9 +809,6 @@
     <test expect_num_outputs="3">
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
-        <param name="fragment_bin_tolerance" value="1.0005"/>
-        <param name="fragment_bin_offset" value="0.25"/>
-        <param name="instrument" value="high_res"/>
         <param name="use_A_ions" value="false"/>
         <param name="use_B_ions" value="true"/>
         <param name="use_C_ions" value="false"/>
@@ -823,6 +816,7 @@
         <param name="use_Y_ions" value="true"/>
         <param name="use_Z_ions" value="false"/>
         <param name="use_NL_ions" value="false"/>
+        <param name="second_enzyme" value=""/>
         <param name="digest_mass_range" value="600:5000"/>
         <param name="max_precursor_charge" value="5"/>
         <param name="spectrum_batch_size" value="1000"/>
@@ -834,7 +828,7 @@
         <param name="clear_mz_range" value="0:0"/>
         <param name="max_variable_mods_in_peptide" value="5"/>
         <param name="require_variable_mod" value="false"/>
-        <param name="force" value="false"/>
+        <param name="force" value="true"/>
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="CometAdapter_2_prepared.mzML"/>
@@ -844,9 +838,15 @@
       <param name="precursor_mass_tolerance" value="3.0"/>
       <param name="precursor_error_units" value="Da"/>
       <param name="isotope_error" value="off"/>
+      <param name="fragment_mass_tolerance" value="0.50025"/>
+      <param name="fragment_error_units" value="Da"/>
+      <param name="fragment_bin_offset" value="0.25"/>
+      <param name="instrument" value="high_res"/>
       <param name="enzyme" value="Trypsin"/>
       <param name="num_enzyme_termini" value="fully"/>
-      <param name="allowed_missed_cleavages" value="1"/>
+      <param name="missed_cleavages" value="1"/>
+      <param name="min_peptide_length" value="5"/>
+      <param name="max_peptide_length" value="63"/>
       <param name="num_hits" value="5"/>
       <param name="precursor_charge" value="0:0"/>
       <param name="override_charge" value="keep any known"/>
@@ -856,6 +856,7 @@
       <param name="clip_nterm_methionine" value="false"/>
       <param name="fixed_modifications" value=""/>
       <param name="variable_modifications" value=""/>
+      <param name="binary_modifications" value=""/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
@@ -866,9 +867,6 @@
     <test expect_num_outputs="3">
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
-        <param name="fragment_bin_tolerance" value="0.02"/>
-        <param name="fragment_bin_offset" value="0.0"/>
-        <param name="instrument" value="high_res"/>
         <param name="use_A_ions" value="false"/>
         <param name="use_B_ions" value="true"/>
         <param name="use_C_ions" value="false"/>
@@ -876,6 +874,7 @@
         <param name="use_Y_ions" value="true"/>
         <param name="use_Z_ions" value="false"/>
         <param name="use_NL_ions" value="false"/>
+        <param name="second_enzyme" value=""/>
         <param name="digest_mass_range" value="600:5000"/>
         <param name="max_precursor_charge" value="5"/>
         <param name="spectrum_batch_size" value="20000"/>
@@ -897,9 +896,15 @@
       <param name="precursor_mass_tolerance" value="5.0"/>
       <param name="precursor_error_units" value="ppm"/>
       <param name="isotope_error" value="off"/>
+      <param name="fragment_mass_tolerance" value="0.01"/>
+      <param name="fragment_error_units" value="Da"/>
+      <param name="fragment_bin_offset" value="0.0"/>
+      <param name="instrument" value="high_res"/>
       <param name="enzyme" value="Trypsin"/>
       <param name="num_enzyme_termini" value="fully"/>
-      <param name="allowed_missed_cleavages" value="3"/>
+      <param name="missed_cleavages" value="3"/>
+      <param name="min_peptide_length" value="5"/>
+      <param name="max_peptide_length" value="63"/>
       <param name="num_hits" value="5"/>
       <param name="precursor_charge" value="0:0"/>
       <param name="override_charge" value="keep known search unknown"/>
@@ -909,6 +914,7 @@
       <param name="clip_nterm_methionine" value="false"/>
       <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
       <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term)"/>
+      <param name="binary_modifications" value=""/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
@@ -916,6 +922,63 @@
         </assert_contents>
       </output>
     </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="use_A_ions" value="false"/>
+        <param name="use_B_ions" value="true"/>
+        <param name="use_C_ions" value="false"/>
+        <param name="use_X_ions" value="false"/>
+        <param name="use_Y_ions" value="true"/>
+        <param name="use_Z_ions" value="false"/>
+        <param name="use_NL_ions" value="false"/>
+        <param name="second_enzyme" value=""/>
+        <param name="digest_mass_range" value="600:1200"/>
+        <param name="max_precursor_charge" value="5"/>
+        <param name="spectrum_batch_size" value="20000"/>
+        <param name="mass_offsets" value="0.0"/>
+        <param name="minimum_peaks" value="10"/>
+        <param name="minimum_intensity" value="0.0"/>
+        <param name="remove_precursor_peak" value="no"/>
+        <param name="remove_precursor_tolerance" value="1.5"/>
+        <param name="clear_mz_range" value="0:0"/>
+        <param name="max_variable_mods_in_peptide" value="3"/>
+        <param name="require_variable_mod" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="examples/FRACTIONS/BSA1_F1.mzML"/>
+      <output name="out" file="CometAdapter_4_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="database" value="examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta"/>
+      <param name="precursor_mass_tolerance" value="5.0"/>
+      <param name="precursor_error_units" value="ppm"/>
+      <param name="isotope_error" value="off"/>
+      <param name="fragment_mass_tolerance" value="0.01"/>
+      <param name="fragment_error_units" value="Da"/>
+      <param name="fragment_bin_offset" value="0.0"/>
+      <param name="instrument" value="high_res"/>
+      <param name="enzyme" value="Trypsin"/>
+      <param name="num_enzyme_termini" value="fully"/>
+      <param name="missed_cleavages" value="3"/>
+      <param name="min_peptide_length" value="5"/>
+      <param name="max_peptide_length" value="63"/>
+      <param name="num_hits" value="5"/>
+      <param name="precursor_charge" value="0:0"/>
+      <param name="override_charge" value="keep known search unknown"/>
+      <param name="ms_level" value="2"/>
+      <param name="activation_method" value="ALL"/>
+      <param name="max_fragment_charge" value="3"/>
+      <param name="clip_nterm_methionine" value="false"/>
+      <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
+      <param name="variable_modifications" value="Met-loss (Protein N-term M)"/>
+      <param name="binary_modifications" value=""/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </xml>
   <xml name="autotest_CompNovoCID">
     <test expect_num_outputs="2">
@@ -1006,11 +1069,13 @@
       <output name="out" file="ConsensusID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="false"/>
       <param name="algorithm" value="PEPMatrix"/>
       <section name="filter">
         <param name="considered_hits" value="0"/>
         <param name="min_support" value="0.0"/>
         <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="false"/>
       </section>
       <section name="PEPIons">
         <param name="mass_tolerance" value="0.5"/>
@@ -1037,11 +1102,13 @@
       <output name="out" file="ConsensusID_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="false"/>
       <param name="algorithm" value="average"/>
       <section name="filter">
         <param name="considered_hits" value="0"/>
         <param name="min_support" value="0.0"/>
         <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="false"/>
       </section>
       <section name="PEPIons">
         <param name="mass_tolerance" value="0.5"/>
@@ -1068,11 +1135,13 @@
       <output name="out" file="ConsensusID_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="false"/>
       <param name="algorithm" value="best"/>
       <section name="filter">
         <param name="considered_hits" value="0"/>
         <param name="min_support" value="0.0"/>
         <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="false"/>
       </section>
       <section name="PEPIons">
         <param name="mass_tolerance" value="0.5"/>
@@ -1099,11 +1168,13 @@
       <output name="out" file="ConsensusID_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="false"/>
       <param name="algorithm" value="PEPMatrix"/>
       <section name="filter">
         <param name="considered_hits" value="6"/>
         <param name="min_support" value="0.0"/>
         <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="false"/>
       </section>
       <section name="PEPIons">
         <param name="mass_tolerance" value="0.5"/>
@@ -1130,11 +1201,13 @@
       <output name="out" file="ConsensusID_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="false"/>
       <param name="algorithm" value="PEPIons"/>
       <section name="filter">
         <param name="considered_hits" value="0"/>
         <param name="min_support" value="0.0"/>
         <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="false"/>
       </section>
       <section name="PEPIons">
         <param name="mass_tolerance" value="0.5"/>
@@ -1161,11 +1234,79 @@
       <output name="out" file="ConsensusID_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="false"/>
       <param name="algorithm" value="best"/>
       <section name="filter">
         <param name="considered_hits" value="0"/>
         <param name="min_support" value="0.5"/>
         <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="false"/>
+      </section>
+      <section name="PEPIons">
+        <param name="mass_tolerance" value="0.5"/>
+        <param name="min_shared" value="2"/>
+      </section>
+      <section name="PEPMatrix">
+        <param name="matrix" value="identity"/>
+        <param name="penalty" value="5"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="ConsensusID_6_input.idXML"/>
+      <output name="out" file="ConsensusID_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="rt_delta" value="0.1"/>
+      <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="true"/>
+      <param name="algorithm" value="best"/>
+      <section name="filter">
+        <param name="considered_hits" value="0"/>
+        <param name="min_support" value="0.0"/>
+        <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="true"/>
+      </section>
+      <section name="PEPIons">
+        <param name="mass_tolerance" value="0.5"/>
+        <param name="min_shared" value="2"/>
+      </section>
+      <section name="PEPMatrix">
+        <param name="matrix" value="identity"/>
+        <param name="penalty" value="5"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="ConsensusID_8_input.idXML"/>
+      <output name="out" file="ConsensusID_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="rt_delta" value="0.1"/>
+      <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="true"/>
+      <param name="algorithm" value="best"/>
+      <section name="filter">
+        <param name="considered_hits" value="0"/>
+        <param name="min_support" value="0.0"/>
+        <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="true"/>
       </section>
       <section name="PEPIons">
         <param name="mass_tolerance" value="0.5"/>
@@ -1230,7 +1371,7 @@
       <param name="enzyme" value="trypsin"/>
       <param name="digestion" value="full-digest"/>
       <param name="allowed_missed_cleavages" value="0"/>
-      <param name="decoy_format" value="shuffle"/>
+      <param name="decoy_format" value="peptide-reverse"/>
       <param name="keep_terminal_aminos" value="NC"/>
       <param name="cterm_modifications" value=""/>
       <param name="nterm_modifications" value=""/>
@@ -1317,6 +1458,74 @@
       </output>
     </test>
   </xml>
+  <xml name="autotest_DatabaseSuitability">
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
+      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
+      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
+      <output name="out" file="DatabaseSuitability_out_1.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
+      <section name="algorithm">
+        <param name="no_rerank" value="false"/>
+        <param name="reranking_cutoff_percentile" value="0.01"/>
+        <param name="FDR" value="0.8"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
+      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
+      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
+      <output name="out" file="DatabaseSuitability_out_2.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
+      <section name="algorithm">
+        <param name="no_rerank" value="false"/>
+        <param name="reranking_cutoff_percentile" value="0.9"/>
+        <param name="FDR" value="1.0"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
+      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
+      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
+      <output name="out" file="DatabaseSuitability_out_3.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
+      <section name="algorithm">
+        <param name="no_rerank" value="true"/>
+        <param name="reranking_cutoff_percentile" value="0.01"/>
+        <param name="FDR" value="0.9"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+  </xml>
   <xml name="autotest_Decharger">
     <test expect_num_outputs="4">
       <conditional name="adv_opts_cond">
@@ -1475,6 +1684,8 @@
   </xml>
   <xml name="autotest_DeMeanderize">
 </xml>
+  <xml name="autotest_DigestorMotif">
+</xml>
   <xml name="autotest_Digestor">
 </xml>
   <xml name="autotest_DTAExtractor">
@@ -1546,12 +1757,14 @@
       </conditional>
       <param name="in" value="FidoAdapter_1_input.idXML"/>
       <output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="out_type" value="idxml"/>
       <param name="protein_fdr" value="false"/>
       <param name="greedy_group_resolution" value="none"/>
       <param name="max_psms_extreme_probability" value="1.0"/>
       <section name="algorithm">
         <param name="psm_probability_cutoff" value="0.001"/>
         <param name="top_PSMs" value="1"/>
+        <param name="keep_best_PSM_only" value="true"/>
         <param name="update_PSM_probabilities" value="true"/>
         <param name="user_defined_priors" value="false"/>
         <param name="annotate_group_probabilities" value="true"/>
@@ -1574,6 +1787,107 @@
         <section name="param_optimize">
           <param name="aucweight" value="0.3"/>
           <param name="conservative_fdr" value="true"/>
+          <param name="regularized_fdr" value="true"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="conservative_fdr" value="true"/>
+        <param name="min_psms_extreme_probability" value="0.0"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="Epifany_2_input.consensusXML"/>
+      <output name="out" file="Epifany_2_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
+      <param name="out_type" value="consensusXML"/>
+      <param name="protein_fdr" value="false"/>
+      <param name="greedy_group_resolution" value="none"/>
+      <param name="max_psms_extreme_probability" value="1.0"/>
+      <section name="algorithm">
+        <param name="psm_probability_cutoff" value="0.001"/>
+        <param name="top_PSMs" value="1"/>
+        <param name="keep_best_PSM_only" value="true"/>
+        <param name="update_PSM_probabilities" value="true"/>
+        <param name="user_defined_priors" value="false"/>
+        <param name="annotate_group_probabilities" value="true"/>
+        <param name="use_ids_outside_features" value="false"/>
+        <section name="model_parameters">
+          <param name="prot_prior" value="0.7"/>
+          <param name="pep_emission" value="0.1"/>
+          <param name="pep_spurious_emission" value="0.001"/>
+          <param name="pep_prior" value="0.1"/>
+          <param name="regularize" value="false"/>
+          <param name="extended_model" value="false"/>
+        </section>
+        <section name="loopy_belief_propagation">
+          <param name="scheduling_type" value="priority"/>
+          <param name="convergence_threshold" value="1e-05"/>
+          <param name="dampening_lambda" value="0.001"/>
+          <param name="max_nr_iterations" value="2147483647"/>
+          <param name="p_norm_inference" value="1.0"/>
+        </section>
+        <section name="param_optimize">
+          <param name="aucweight" value="0.3"/>
+          <param name="conservative_fdr" value="true"/>
+          <param name="regularized_fdr" value="true"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="conservative_fdr" value="true"/>
+        <param name="min_psms_extreme_probability" value="0.0"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="Epifany_2_input.consensusXML"/>
+      <output name="out" file="Epifany_3_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
+      <param name="out_type" value="consensusXML"/>
+      <param name="protein_fdr" value="false"/>
+      <param name="greedy_group_resolution" value="none"/>
+      <param name="max_psms_extreme_probability" value="1.0"/>
+      <section name="algorithm">
+        <param name="psm_probability_cutoff" value="0.001"/>
+        <param name="top_PSMs" value="1"/>
+        <param name="keep_best_PSM_only" value="false"/>
+        <param name="update_PSM_probabilities" value="true"/>
+        <param name="user_defined_priors" value="false"/>
+        <param name="annotate_group_probabilities" value="true"/>
+        <param name="use_ids_outside_features" value="false"/>
+        <section name="model_parameters">
+          <param name="prot_prior" value="0.7"/>
+          <param name="pep_emission" value="0.1"/>
+          <param name="pep_spurious_emission" value="0.001"/>
+          <param name="pep_prior" value="0.1"/>
+          <param name="regularize" value="false"/>
+          <param name="extended_model" value="false"/>
+        </section>
+        <section name="loopy_belief_propagation">
+          <param name="scheduling_type" value="priority"/>
+          <param name="convergence_threshold" value="1e-05"/>
+          <param name="dampening_lambda" value="0.001"/>
+          <param name="max_nr_iterations" value="2147483647"/>
+          <param name="p_norm_inference" value="1.0"/>
+        </section>
+        <section name="param_optimize">
+          <param name="aucweight" value="0.3"/>
+          <param name="conservative_fdr" value="true"/>
+          <param name="regularized_fdr" value="true"/>
         </section>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -1976,6 +2290,7 @@
         <param name="add_zeros" value="0.2"/>
         <param name="unweighted_fit" value="false"/>
         <param name="no_imputation" value="false"/>
+        <param name="each_trace" value="false"/>
         <section name="check">
           <param name="min_area" value="1.0"/>
           <param name="boundaries" value="0.5"/>
@@ -2031,61 +2346,7 @@
         <param name="add_zeros" value="0.2"/>
         <param name="unweighted_fit" value="false"/>
         <param name="no_imputation" value="false"/>
-        <section name="check">
-          <param name="min_area" value="1.0"/>
-          <param name="boundaries" value="0.5"/>
-          <param name="width" value="10.0"/>
-          <param name="asymmetry" value="10.0"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
-      <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
-      <output name="out" file="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="extract">
-        <param name="batch_size" value="10"/>
-        <param name="mz_window" value="0.1"/>
-        <param name="n_isotopes" value="2"/>
-        <param name="isotope_pmin" value="0.0"/>
-        <param name="rt_quantile" value="0.95"/>
-        <param name="rt_window" value="0.0"/>
-      </section>
-      <section name="detect">
-        <param name="peak_width" value="60.0"/>
-        <param name="min_peak_width" value="0.2"/>
-        <param name="signal_to_noise" value="0.8"/>
-        <param name="mapping_tolerance" value="0.0"/>
-      </section>
-      <section name="svm">
-        <param name="samples" value="0"/>
-        <param name="no_selection" value="false"/>
-        <param name="kernel" value="RBF"/>
-        <param name="xval" value="5"/>
-        <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
-        <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
-        <param name="epsilon" value="0.001"/>
-        <param name="cache_size" value="100.0"/>
-        <param name="no_shrinking" value="false"/>
-        <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/>
-        <param name="min_prob" value="0.0"/>
-      </section>
-      <section name="model">
-        <param name="type" value="none"/>
-        <param name="add_zeros" value="0.2"/>
-        <param name="unweighted_fit" value="false"/>
-        <param name="no_imputation" value="false"/>
+        <param name="each_trace" value="false"/>
         <section name="check">
           <param name="min_area" value="1.0"/>
           <param name="boundaries" value="0.5"/>
@@ -2129,6 +2390,7 @@
         <param name="add_zeros" value="0.2"/>
         <param name="unweighted_fit" value="false"/>
         <param name="no_imputation" value="false"/>
+        <param name="each_trace" value="false"/>
         <section name="check">
           <param name="min_area" value="1.0"/>
           <param name="boundaries" value="0.5"/>
@@ -4074,7 +4336,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="FidoAdapter_1_input.idXML"/>
-      <output name="out" file="FidoAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <output name="out" file="FidoAdapter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
       <param name="separate_runs" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="no_cleanup" value="false"/>
@@ -5009,6 +5271,34 @@
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
+      <param name="in" value="FileConverter_32_input.mzML"/>
+      <output name="out" file="FileConverter_32_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
+      <param name="out_type" value="mzML"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="UID_postprocessing" value="ensure"/>
+        <param name="TIC_DTA2D" value="false"/>
+        <param name="MGF_compact" value="false"/>
+        <param name="force_MaxQuant_compatibility" value="false"/>
+        <param name="convert_to_chromatograms" value="false"/>
+        <param name="force_TPP_compatibility" value="false"/>
+        <param name="change_im_format" value="none"/>
+        <param name="write_scan_index" value="true"/>
+        <param name="lossy_compression" value="false"/>
+        <param name="lossy_mass_accuracy" value="-1.0"/>
+        <param name="process_lowmemory" value="false"/>
+        <param name="no_peak_picking" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
       <param name="in" value="ginkgotoxin-ms-switching.raw"/>
       <output name="out" file="ginkgotoxin-ms-switching_out_tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
       <param name="out_type" value="mzml"/>
@@ -11129,6 +11419,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11154,6 +11446,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11179,6 +11473,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11203,6 +11499,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11228,6 +11526,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11253,6 +11553,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11277,6 +11579,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11301,6 +11605,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11325,6 +11631,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11349,6 +11657,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11373,6 +11683,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11397,6 +11709,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11421,6 +11735,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11445,6 +11761,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11470,6 +11788,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11494,6 +11814,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11518,6 +11840,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11542,6 +11866,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11566,6 +11892,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11590,6 +11918,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11615,6 +11945,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.01"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11640,6 +11972,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11664,6 +11998,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11688,6 +12024,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11712,6 +12050,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11728,6 +12068,136 @@
         </assert_contents>
       </output>
     </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="ignore_proteins_per_peptide" value="false"/>
+        <param name="scan_regex" value=""/>
+        <param name="no_spectra_data_override" value="false"/>
+        <param name="no_spectra_references_override" value="false"/>
+        <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="IDFileConverter_27_input.idXML"/>
+      <output name="out" file="IDFileConverter_27_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
+      <param name="out_type" value="FASTA"/>
+      <param name="mz_name" value=""/>
+      <param name="peptideprophet_analyzed" value="false"/>
+      <param name="score_type" value="qvalue"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="ignore_proteins_per_peptide" value="false"/>
+        <param name="scan_regex" value=""/>
+        <param name="no_spectra_data_override" value="false"/>
+        <param name="no_spectra_references_override" value="false"/>
+        <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="-1"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="IDFileConverter_27_input.idXML"/>
+      <output name="out" file="IDFileConverter_28_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
+      <param name="out_type" value="FASTA"/>
+      <param name="mz_name" value=""/>
+      <param name="peptideprophet_analyzed" value="false"/>
+      <param name="score_type" value="qvalue"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="ignore_proteins_per_peptide" value="false"/>
+        <param name="scan_regex" value=""/>
+        <param name="no_spectra_data_override" value="false"/>
+        <param name="no_spectra_references_override" value="false"/>
+        <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="true"/>
+        <param name="number_of_hits" value="1"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="IDFileConverter_27_input.idXML"/>
+      <output name="out" file="IDFileConverter_29_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
+      <param name="out_type" value="FASTA"/>
+      <param name="mz_name" value=""/>
+      <param name="peptideprophet_analyzed" value="false"/>
+      <param name="score_type" value="qvalue"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="ignore_proteins_per_peptide" value="false"/>
+        <param name="scan_regex" value=""/>
+        <param name="no_spectra_data_override" value="false"/>
+        <param name="no_spectra_references_override" value="false"/>
+        <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="true"/>
+        <param name="number_of_hits" value="2"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="IDFileConverter_27_input.idXML"/>
+      <output name="out" file="IDFileConverter_30_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
+      <param name="out_type" value="FASTA"/>
+      <param name="mz_name" value=""/>
+      <param name="peptideprophet_analyzed" value="false"/>
+      <param name="score_type" value="qvalue"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="ignore_proteins_per_peptide" value="false"/>
+        <param name="scan_regex" value=""/>
+        <param name="no_spectra_data_override" value="false"/>
+        <param name="no_spectra_references_override" value="false"/>
+        <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="IDFileConverter_31_input.mzid"/>
+      <output name="out" file="IDFileConverter_31_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="out_type" value="idXML"/>
+      <param name="mz_name" value=""/>
+      <param name="peptideprophet_analyzed" value="false"/>
+      <param name="score_type" value="qvalue"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </xml>
   <xml name="autotest_IDFilter">
     <test expect_num_outputs="2">
@@ -11754,6 +12224,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="proteins" value="IDFilter_1_input.fas"/>
@@ -11821,6 +12292,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -11888,6 +12360,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -11954,6 +12427,7 @@
       <section name="score">
         <param name="pep" value="32.0"/>
         <param name="prot" value="25.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12020,6 +12494,7 @@
       <section name="score">
         <param name="pep" value="32.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12086,6 +12561,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="25.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12152,6 +12628,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="25.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12218,6 +12695,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12284,6 +12762,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12350,6 +12829,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12416,6 +12896,7 @@
       <section name="score">
         <param name="pep" value="0.05"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12482,6 +12963,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.3"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12548,6 +13030,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12614,6 +13097,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12681,6 +13165,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12748,6 +13233,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12815,6 +13301,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12882,6 +13369,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12949,6 +13437,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -13015,6 +13504,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -13081,6 +13571,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -13147,6 +13638,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -13213,6 +13705,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -13279,6 +13772,141 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
+      </section>
+      <section name="whitelist">
+        <param name="protein_accessions" value=""/>
+        <param name="ignore_modifications" value="false"/>
+        <param name="modifications" value=""/>
+      </section>
+      <section name="blacklist">
+        <param name="protein_accessions" value=""/>
+        <param name="ignore_modifications" value="false"/>
+        <param name="modifications" value=""/>
+      </section>
+      <section name="in_silico_digestion">
+        <param name="enzyme" value="Trypsin"/>
+        <param name="specificity" value="full"/>
+        <param name="missed_cleavages" value="-1"/>
+        <param name="methionine_cleavage" value="false"/>
+      </section>
+      <section name="missed_cleavages">
+        <param name="number_of_missed_cleavages" value=":"/>
+        <param name="enzyme" value="Trypsin"/>
+      </section>
+      <section name="rt">
+        <param name="p_value" value="0.0"/>
+        <param name="p_value_1st_dim" value="0.0"/>
+      </section>
+      <section name="mz">
+        <param name="error" value="-1.0"/>
+        <param name="unit" value="ppm"/>
+      </section>
+      <section name="best">
+        <param name="n_peptide_hits" value="0"/>
+        <param name="n_protein_hits" value="0"/>
+        <param name="strict" value="false"/>
+        <param name="n_to_m_peptide_hits" value=":"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="remove_duplicate_psm" value="false"/>
+        <param name="remove_peptide_hits_by_metavalue" value=""/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="IDMapper_2_output.consensusXML"/>
+      <output name="out" file="IDFilter_23_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
+      <param name="var_mods" value="false"/>
+      <param name="remove_shared_peptides" value="false"/>
+      <param name="keep_unreferenced_protein_hits" value="false"/>
+      <param name="remove_decoys" value="false"/>
+      <param name="delete_unreferenced_peptide_hits" value="false"/>
+      <section name="precursor">
+        <param name="rt" value=":"/>
+        <param name="mz" value=":"/>
+        <param name="length" value=":"/>
+        <param name="charge" value=":"/>
+      </section>
+      <section name="score">
+        <param name="pep" value="0.0"/>
+        <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
+      </section>
+      <section name="whitelist">
+        <param name="protein_accessions" value="&quot;Q9HP81&quot;"/>
+        <param name="ignore_modifications" value="false"/>
+        <param name="modifications" value=""/>
+      </section>
+      <section name="blacklist">
+        <param name="protein_accessions" value=""/>
+        <param name="ignore_modifications" value="false"/>
+        <param name="modifications" value=""/>
+      </section>
+      <section name="in_silico_digestion">
+        <param name="enzyme" value="Trypsin"/>
+        <param name="specificity" value="full"/>
+        <param name="missed_cleavages" value="-1"/>
+        <param name="methionine_cleavage" value="false"/>
+      </section>
+      <section name="missed_cleavages">
+        <param name="number_of_missed_cleavages" value=":"/>
+        <param name="enzyme" value="Trypsin"/>
+      </section>
+      <section name="rt">
+        <param name="p_value" value="0.0"/>
+        <param name="p_value_1st_dim" value="0.0"/>
+      </section>
+      <section name="mz">
+        <param name="error" value="-1.0"/>
+        <param name="unit" value="ppm"/>
+      </section>
+      <section name="best">
+        <param name="n_peptide_hits" value="0"/>
+        <param name="n_protein_hits" value="0"/>
+        <param name="strict" value="false"/>
+        <param name="n_to_m_peptide_hits" value=":"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="remove_duplicate_psm" value="false"/>
+        <param name="remove_peptide_hits_by_metavalue" value=""/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="Epifany_3_out.consensusXML"/>
+      <output name="out" file="IDFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
+      <param name="var_mods" value="false"/>
+      <param name="remove_shared_peptides" value="false"/>
+      <param name="keep_unreferenced_protein_hits" value="false"/>
+      <param name="remove_decoys" value="false"/>
+      <param name="delete_unreferenced_peptide_hits" value="false"/>
+      <section name="precursor">
+        <param name="rt" value=":"/>
+        <param name="mz" value=":"/>
+        <param name="length" value=":"/>
+        <param name="charge" value=":"/>
+      </section>
+      <section name="score">
+        <param name="pep" value="0.0"/>
+        <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.99"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -13882,11 +14510,11 @@
       </conditional>
       <param name="in" value="IDFileConverter_12_output.idXML"/>
       <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="proteins" value="false"/>
       <param name="new_score" value="Percolator_PEP"/>
       <param name="new_score_orientation" value="lower_better"/>
       <param name="new_score_type" value="Posterior Error Probability"/>
       <param name="old_score" value="Percolator_qvalue"/>
-      <param name="proteins" value="false"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
@@ -13902,11 +14530,11 @@
       </conditional>
       <param name="in" value="IDScoreSwitcher_2_input.idXML"/>
       <output name="out" file="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="proteins" value="true"/>
       <param name="new_score" value="Posterior Probability_score"/>
       <param name="new_score_orientation" value="higher_better"/>
       <param name="new_score_type" value="Posterior Probability"/>
       <param name="old_score" value=""/>
-      <param name="proteins" value="true"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
@@ -14453,80 +15081,6 @@
   </xml>
   <xml name="autotest_LabeledEval">
 </xml>
-  <xml name="autotest_LowMemPeakPickerHiResRandomAccess">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerHiRes_RandomAccess_input.mzML"/>
-      <output name="out" file="LowMemPeakPickerHiRes_RandomAccess_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="1.0"/>
-        <param name="spacing_difference_gap" value="4.0"/>
-        <param name="spacing_difference" value="1.5"/>
-        <param name="missing" value="1"/>
-        <param name="ms_levels" value="1"/>
-        <param name="report_FWHM" value="false"/>
-        <param name="report_FWHM_unit" value="relative"/>
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_LowMemPeakPickerHiRes">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerHiRes_input.mzML"/>
-      <output name="out" file="LowMemPeakPickerHiRes_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="1.0"/>
-        <param name="spacing_difference_gap" value="4.0"/>
-        <param name="spacing_difference" value="1.5"/>
-        <param name="missing" value="1"/>
-        <param name="ms_levels" value="1"/>
-        <param name="report_FWHM" value="false"/>
-        <param name="report_FWHM_unit" value="relative"/>
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
   <xml name="autotest_LuciphorAdapter">
     <test expect_num_outputs="2">
       <conditional name="adv_opts_cond">
@@ -14894,6 +15448,63 @@
         </assert_contents>
       </output>
     </test>
+    <test expect_num_outputs="3">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="true"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MapAlignerIdentification_7_input1.idXML"/>
+      <output_collection name="out" count="1"/>
+      <output_collection name="trafo_out" count="1"/>
+      <section name="reference">
+        <param name="file" value="MapAlignerIdentification_7_input2.idXML"/>
+        <param name="index" value="0"/>
+      </section>
+      <section name="algorithm">
+        <param name="score_cutoff" value="false"/>
+        <param name="min_score" value="0.05"/>
+        <param name="min_run_occur" value="2"/>
+        <param name="max_rt_shift" value="0.5"/>
+        <param name="use_unassigned_peptides" value="true"/>
+        <param name="use_feature_rt" value="false"/>
+      </section>
+      <section name="model">
+        <param name="type" value="b_spline"/>
+        <section name="linear">
+          <param name="symmetric_regression" value="false"/>
+          <param name="x_weight" value=""/>
+          <param name="y_weight" value=""/>
+          <param name="x_datum_min" value="1e-15"/>
+          <param name="x_datum_max" value="1000000000000000.0"/>
+          <param name="y_datum_min" value="1e-15"/>
+          <param name="y_datum_max" value="1000000000000000.0"/>
+        </section>
+        <section name="b_spline">
+          <param name="wavelength" value="0.0"/>
+          <param name="num_nodes" value="5"/>
+          <param name="extrapolate" value="linear"/>
+          <param name="boundary_condition" value="2"/>
+        </section>
+        <section name="lowess">
+          <param name="span" value="0.666666666666667"/>
+          <param name="num_iterations" value="3"/>
+          <param name="delta" value="-1.0"/>
+          <param name="interpolation_type" value="cspline"/>
+          <param name="extrapolation_type" value="four-point-linear"/>
+        </section>
+        <section name="interpolated">
+          <param name="interpolation_type" value="cspline"/>
+          <param name="extrapolation_type" value="two-point-linear"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </xml>
   <xml name="autotest_MapAlignerPoseClustering">
     <test expect_num_outputs="3">
@@ -15281,6 +15892,61 @@
         </assert_contents>
       </output>
     </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/>
+      <output_collection name="out" count="3"/>
+      <section name="algorithm">
+        <param name="model_type" value="b_spline"/>
+        <section name="model">
+          <param name="type" value="b_spline"/>
+          <section name="linear">
+            <param name="symmetric_regression" value="false"/>
+            <param name="x_weight" value=""/>
+            <param name="y_weight" value=""/>
+            <param name="x_datum_min" value="1e-15"/>
+            <param name="x_datum_max" value="1000000000000000.0"/>
+            <param name="y_datum_min" value="1e-15"/>
+            <param name="y_datum_max" value="1000000000000000.0"/>
+          </section>
+          <section name="b_spline">
+            <param name="wavelength" value="0.0"/>
+            <param name="num_nodes" value="5"/>
+            <param name="extrapolate" value="linear"/>
+            <param name="boundary_condition" value="2"/>
+          </section>
+          <section name="lowess">
+            <param name="span" value="0.666666666666667"/>
+            <param name="num_iterations" value="3"/>
+            <param name="delta" value="-1.0"/>
+            <param name="interpolation_type" value="cspline"/>
+            <param name="extrapolation_type" value="four-point-linear"/>
+          </section>
+          <section name="interpolated">
+            <param name="interpolation_type" value="cspline"/>
+            <param name="extrapolation_type" value="two-point-linear"/>
+          </section>
+        </section>
+        <section name="align_algorithm">
+          <param name="score_cutoff" value="false"/>
+          <param name="min_score" value="0.05"/>
+          <param name="min_run_occur" value="2"/>
+          <param name="max_rt_shift" value="0.5"/>
+          <param name="use_unassigned_peptides" value="true"/>
+          <param name="use_feature_rt" value="true"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </xml>
   <xml name="autotest_MapNormalizer">
     <test expect_num_outputs="2">
@@ -15651,9 +16317,8 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="MascotAdapter_1_input.mzData"/>
-      <output name="out" file="output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="mascot_in" value="true"/>
-      <param name="mascot_out" value="false"/>
+      <output name="out" file="MascotAdapter_1_output.mascot_in" compare="sim_size" delta="5700"/>
+      <param name="out_type" value="mgf"/>
       <param name="instrument" value="ESI-TRAP"/>
       <param name="precursor_mass_tolerance" value="1.3"/>
       <param name="peak_mass_tolerance" value="0.3"/>
@@ -15691,8 +16356,7 @@
       </conditional>
       <param name="in" value="MascotAdapter_2_input.mascotXML"/>
       <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="mascot_in" value="false"/>
-      <param name="mascot_out" value="true"/>
+      <param name="out_type" value="idXML"/>
       <param name="instrument" value="Default"/>
       <param name="precursor_mass_tolerance" value="2.0"/>
       <param name="peak_mass_tolerance" value="1.0"/>
@@ -15730,9 +16394,9 @@
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
-      <param name="in" value="MassCalculator_1_input.txt" ftype="txt"/>
+      <param name="in" value="MassCalculator_1_input.tsv" ftype="tabular"/>
       <param name="in_seq" value=""/>
-      <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta="5700" ftype="txt"/>
+      <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta="5700" ftype="csv"/>
       <param name="charge" value="0 1"/>
       <param name="format" value="table"/>
       <param name="average_mass" value="false"/>
@@ -15752,7 +16416,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in_seq" value="&quot;LDQWLC(Carbamidomethyl)EKL&quot; &quot;(Glu-&gt;pyro-Glu)EAM(Oxidation)APKHK&quot; &quot;RANVM(Oxidation)DYR&quot; &quot;FGVEQDVDMVFASFIR&quot;"/>
-      <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
+      <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
       <param name="charge" value="1 2 3"/>
       <param name="format" value="list"/>
       <param name="average_mass" value="false"/>
@@ -15849,7 +16513,80 @@
     </test>
   </xml>
   <xml name="autotest_MetaboliteAdductDecharger">
-</xml>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/>
+      <output name="out_fm" file="MetaboliteAdductDecharger_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
+      <section name="algorithm">
+        <section name="MetaboliteFeatureDeconvolution">
+          <param name="charge_min" value="1"/>
+          <param name="charge_max" value="3"/>
+          <param name="charge_span_max" value="3"/>
+          <param name="q_try" value="feature"/>
+          <param name="retention_max_diff" value="1.0"/>
+          <param name="retention_max_diff_local" value="1.0"/>
+          <param name="mass_max_diff" value="0.05"/>
+          <param name="unit" value="Da"/>
+          <param name="potential_adducts" value="&quot;H:+:0.4&quot; &quot;Na:+:0.25&quot; &quot;NH4:+:0.25&quot; &quot;K:+:0.1&quot; &quot;H-2O-1:0:0.05&quot;"/>
+          <param name="max_neutrals" value="1"/>
+          <param name="use_minority_bound" value="true"/>
+          <param name="max_minority_bound" value="3"/>
+          <param name="min_rt_overlap" value="0.66"/>
+          <param name="intensity_filter" value="false"/>
+          <param name="negative_mode" value="false"/>
+          <param name="default_map_label" value="decharged features"/>
+          <param name="verbose_level" value="0"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="3">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/>
+      <output name="out_cm" file="MetaboliteAdductDecharger_2_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
+      <output name="outpairs" file="MetaboliteAdductDecharger_2_output_2.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
+      <section name="algorithm">
+        <section name="MetaboliteFeatureDeconvolution">
+          <param name="charge_min" value="1"/>
+          <param name="charge_max" value="3"/>
+          <param name="charge_span_max" value="3"/>
+          <param name="q_try" value="feature"/>
+          <param name="retention_max_diff" value="1.0"/>
+          <param name="retention_max_diff_local" value="1.0"/>
+          <param name="mass_max_diff" value="0.05"/>
+          <param name="unit" value="Da"/>
+          <param name="potential_adducts" value="&quot;H:+:0.4&quot; &quot;Na:+:0.25&quot; &quot;NH4:+:0.25&quot; &quot;K:+:0.1&quot; &quot;H-2O-1:0:0.05&quot;"/>
+          <param name="max_neutrals" value="1"/>
+          <param name="use_minority_bound" value="true"/>
+          <param name="max_minority_bound" value="3"/>
+          <param name="min_rt_overlap" value="0.66"/>
+          <param name="intensity_filter" value="false"/>
+          <param name="negative_mode" value="false"/>
+          <param name="default_map_label" value="decharged features"/>
+          <param name="verbose_level" value="0"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_cm_FLAG,outpairs_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+  </xml>
   <xml name="autotest_MetaboliteSpectralMatcher">
 </xml>
   <xml name="autotest_MetaProSIP">
@@ -16055,6 +16792,7 @@
     <test expect_num_outputs="3">
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
+        <param name="add_decoys" value="false"/>
         <param name="legacy_conversion" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -16063,7 +16801,6 @@
       <output name="out" file="MSGFPlusAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
       <output name="mzid_out" file="MSGFPlusAdapter_1_out2.tmp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
       <param name="database" value="proteins.fasta"/>
-      <param name="add_decoys" value="false"/>
       <param name="precursor_mass_tolerance" value="10.0"/>
       <param name="precursor_error_units" value="ppm"/>
       <param name="isotope_error_range" value="0,1"/>
@@ -16079,6 +16816,8 @@
       <param name="matches_per_spec" value="1"/>
       <param name="add_features" value="false"/>
       <param name="max_mods" value="2"/>
+      <param name="max_missed_cleavages" value="-1"/>
+      <param name="tasks" value="0"/>
       <param name="fixed_modifications" value=""/>
       <param name="variable_modifications" value="Oxidation (M)"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mzid_out_FLAG"/>
@@ -16413,6 +17152,74 @@
         </assert_contents>
       </output>
     </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="first_run_inference_only" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="Epifany_2_out.consensusXML"/>
+      <output name="out" file="MzTabExporter_4_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
+      <param name="opt_columns" value="subfeatures"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="first_run_inference_only" value="true"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MzTabExporter_5_in.consensusXML"/>
+      <output name="out" file="MzTabExporter_5_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
+      <param name="opt_columns" value="subfeatures"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="first_run_inference_only" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MzTabExporter_6_input.idXML"/>
+      <output name="out" file="MzTabExporter_6_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
+      <param name="opt_columns" value="subfeatures"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="first_run_inference_only" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MzTabExporter_7_input.consensusXML"/>
+      <output name="out" file="MzTabExporter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
+      <param name="opt_columns" value="subfeatures"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </xml>
   <xml name="autotest_NoiseFilterGaussian">
     <test expect_num_outputs="2">
@@ -16919,6 +17726,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17030,6 +17838,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17141,6 +17950,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17252,6 +18062,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17362,6 +18173,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17473,6 +18285,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17584,6 +18397,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17695,6 +18509,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17806,6 +18621,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -18290,6 +19106,8 @@
       </output>
     </test>
   </xml>
+  <xml name="autotest_OpenSwathDIAPreScoring">
+</xml>
   <xml name="autotest_OpenSwathFeatureXMLToTSV">
     <test expect_num_outputs="2">
       <conditional name="adv_opts_cond">
@@ -18594,6 +19412,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -18715,6 +19534,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -18836,6 +19656,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -18932,17 +19753,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="false"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="false"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -18951,10 +19772,10 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
@@ -18965,8 +19786,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -18994,7 +19815,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -19008,10 +19829,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -19023,7 +19845,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -19067,13 +19889,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -19089,17 +19911,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_2_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="false"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="false"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -19108,10 +19930,10 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_2_input.mzXML"/>
       <param name="tr" value="OpenSwathWorkflow_2_input.TraML"/>
@@ -19121,8 +19943,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -19150,7 +19972,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -19164,10 +19986,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -19179,7 +20002,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -19223,13 +20046,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -19245,17 +20068,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -19264,10 +20087,10 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
@@ -19277,8 +20100,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -19306,7 +20129,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -19320,10 +20143,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -19335,7 +20159,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -19379,13 +20203,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -19401,17 +20225,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -19420,10 +20244,10 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
@@ -19433,8 +20257,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -19462,7 +20286,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -19476,10 +20300,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -19491,7 +20316,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -19535,13 +20360,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -19557,17 +20382,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -19576,10 +20401,10 @@
         <param name="readOptions" value="cache"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
@@ -19589,8 +20414,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -19618,7 +20443,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -19632,10 +20457,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -19647,7 +20473,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -19691,13 +20517,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -19713,17 +20539,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -19732,10 +20558,10 @@
         <param name="readOptions" value="cacheWorkingInMemory"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
@@ -19745,8 +20571,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -19774,7 +20600,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -19788,10 +20614,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -19803,7 +20630,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -19847,13 +20674,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -19868,19 +20695,18 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -19889,21 +20715,22 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
       <param name="tr_type" value=""/>
+      <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/>
       <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
       <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -19931,7 +20758,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -19945,10 +20772,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -19960,7 +20788,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -20004,13 +20832,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -20025,19 +20853,18 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -20046,21 +20873,22 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
         <param name="force" value="true"/>
-        <param name="test" value="true"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
       <param name="tr_type" value=""/>
+      <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/>
       <output name="out_features" file="OpenSwathWorkflow_10.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
       <output name="out_chrom" file="OpenSwathWorkflow_10.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -20088,7 +20916,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -20102,10 +20930,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -20117,7 +20946,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -20161,13 +20990,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -20182,13 +21011,13 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="false"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="false"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
         <param name="irt_mz_extraction_window" value="550.0"/>
@@ -20201,10 +21030,10 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="quadratic_regression_delta_ppm"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_11_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_11_input_2.TraML"/>
@@ -20216,7 +21045,7 @@
       <param name="rt_extraction_window" value="-1.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
       <param name="mz_extraction_window" value="0.2"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -20244,7 +21073,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -20258,10 +21087,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -20273,7 +21103,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -20317,13 +21147,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="true"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -20339,17 +21169,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -20358,10 +21188,10 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_13_input.pqp.tmp"/>
@@ -20371,8 +21201,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -20400,7 +21230,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -20414,10 +21244,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -20429,7 +21260,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -20473,13 +21304,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -20495,17 +21326,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="sqMass"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -20514,10 +21345,10 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_14_input.pqp.tmp"/>
@@ -20527,8 +21358,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -20556,7 +21387,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -20570,10 +21401,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -20585,7 +21417,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -20629,13 +21461,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -20651,17 +21483,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
         <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -20670,7 +21502,7 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
+        <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="2"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -20684,7 +21516,7 @@
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
       <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -20712,7 +21544,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -20726,10 +21558,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -20807,17 +21640,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -20826,10 +21659,10 @@
         <param name="readOptions" value="workingInMemory"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
+        <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="2"/>
         <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_16_input.sqMass"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
@@ -20839,8 +21672,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -20868,7 +21701,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -20882,10 +21715,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -20897,7 +21731,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -20941,13 +21775,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -20962,17 +21796,17 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="false"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -20981,10 +21815,10 @@
         <param name="readOptions" value="workingInMemory"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
@@ -20994,8 +21828,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="0.05"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -21023,7 +21857,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -21037,10 +21871,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -21052,7 +21887,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -21096,13 +21931,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="true"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -21117,17 +21952,17 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="false"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -21136,10 +21971,10 @@
         <param name="readOptions" value="cache"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
@@ -21149,8 +21984,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="0.05"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -21178,7 +22013,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -21192,10 +22027,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -21207,7 +22043,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -21251,13 +22087,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="true"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -21272,17 +22108,17 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="false"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -21291,10 +22127,10 @@
         <param name="readOptions" value="workingInMemory"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_17_input.pqp.tmp"/>
@@ -21304,8 +22140,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="0.05"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -21333,7 +22169,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -21347,10 +22183,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -21362,7 +22199,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -21406,13 +22243,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -21428,16 +22265,16 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
         <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -21446,7 +22283,7 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
+        <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -21459,7 +22296,7 @@
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
       <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -21487,7 +22324,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -21501,10 +22338,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -21582,16 +22420,16 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
         <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -21600,7 +22438,7 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
+        <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -21613,7 +22451,7 @@
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
       <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -21641,7 +22479,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -21655,10 +22493,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -21736,16 +22575,16 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
         <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -21754,7 +22593,7 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
+        <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -21767,7 +22606,7 @@
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
       <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -21795,7 +22634,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -21809,10 +22648,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -21889,17 +22729,17 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
         <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -21908,7 +22748,7 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
+        <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -21923,7 +22763,7 @@
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
       <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <output name="Debugging_irt_trafo" file="OpenSwathWorkflow_21_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
@@ -21952,7 +22792,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.6666666666666666"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -21966,10 +22806,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -22046,17 +22887,17 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="true"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -22065,10 +22906,10 @@
         <param name="readOptions" value="workingInMemory"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
+        <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="3"/>
         <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_22_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_22_input.tsv" ftype="tabular"/>
@@ -22078,8 +22919,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -22107,7 +22948,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -22121,10 +22962,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -22136,7 +22978,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -22180,13 +23022,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -22207,7 +23049,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="PeakPickerHiRes_input.mzML"/>
-      <output name="out" file="PeakPickerHiRes_1.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
+      <output name="out" file="PeakPickerHiRes_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
       <section name="algorithm">
         <param name="signal_to_noise" value="1.0"/>
         <param name="spacing_difference_gap" value="4.0"/>
@@ -22762,12 +23604,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -22792,12 +23634,12 @@
       <param name="write_protein_sequence" value="true"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -22822,12 +23664,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="true"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -22852,12 +23694,12 @@
       <param name="write_protein_sequence" value="true"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="0"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -22882,12 +23724,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -22912,12 +23754,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="3"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -22942,12 +23784,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="full"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -22972,12 +23814,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="semi"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -23002,12 +23844,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="remove"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -23032,13 +23874,13 @@
       <param name="write_protein_sequence" value="true"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="false"/>
+      <param name="unmatched_action" value="error"/>
       <param name="aaa_max" value="3"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="true"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
-        <param name="specificity" value="full"/>
+        <param name="name" value="auto"/>
+        <param name="specificity" value="auto"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -23062,12 +23904,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -23092,13 +23934,13 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="false"/>
+      <param name="unmatched_action" value="error"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
-        <param name="specificity" value="full"/>
+        <param name="name" value="auto"/>
+        <param name="specificity" value="auto"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -23122,12 +23964,12 @@
       <param name="write_protein_sequence" value="true"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="false"/>
+      <param name="unmatched_action" value="error"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -23149,7 +23991,9 @@
         <param name="testFDR" value="0.5"/>
         <param name="trainFDR" value="0.5"/>
         <param name="maxiter" value="10"/>
+        <param name="nested_xval_bins" value="1"/>
         <param name="quick_validation" value="false"/>
+        <param name="static" value="false"/>
         <param name="default_direction" value=""/>
         <param name="verbose" value="2"/>
         <param name="unitnorm" value="false"/>
@@ -23192,7 +24036,9 @@
         <param name="testFDR" value="0.01"/>
         <param name="trainFDR" value="0.01"/>
         <param name="maxiter" value="10"/>
+        <param name="nested_xval_bins" value="1"/>
         <param name="quick_validation" value="false"/>
+        <param name="static" value="false"/>
         <param name="default_direction" value=""/>
         <param name="verbose" value="2"/>
         <param name="unitnorm" value="false"/>
@@ -23235,7 +24081,9 @@
         <param name="testFDR" value="0.01"/>
         <param name="trainFDR" value="0.01"/>
         <param name="maxiter" value="10"/>
+        <param name="nested_xval_bins" value="1"/>
         <param name="quick_validation" value="false"/>
+        <param name="static" value="false"/>
         <param name="default_direction" value=""/>
         <param name="verbose" value="2"/>
         <param name="unitnorm" value="false"/>
@@ -23278,7 +24126,9 @@
         <param name="testFDR" value="0.01"/>
         <param name="trainFDR" value="0.01"/>
         <param name="maxiter" value="10"/>
+        <param name="nested_xval_bins" value="1"/>
         <param name="quick_validation" value="false"/>
+        <param name="static" value="false"/>
         <param name="default_direction" value=""/>
         <param name="verbose" value="2"/>
         <param name="unitnorm" value="false"/>
@@ -23321,7 +24171,9 @@
         <param name="testFDR" value="0.5"/>
         <param name="trainFDR" value="0.5"/>
         <param name="maxiter" value="10"/>
+        <param name="nested_xval_bins" value="1"/>
         <param name="quick_validation" value="false"/>
+        <param name="static" value="false"/>
         <param name="default_direction" value=""/>
         <param name="verbose" value="2"/>
         <param name="unitnorm" value="false"/>
@@ -23539,6 +24391,7 @@
       <param name="annotate_indist_groups" value="true"/>
       <section name="Merging">
         <param name="annotate_origin" value="false"/>
+        <param name="allow_disagreeing_settings" value="false"/>
       </section>
       <section name="Algorithm">
         <param name="min_peptides_per_protein" value="1"/>
@@ -23808,7 +24661,7 @@
         </assert_contents>
       </output>
     </test>
-    <test expect_num_outputs="2">
+    <test expect_num_outputs="3">
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="force" value="false"/>
@@ -23816,6 +24669,7 @@
       </conditional>
       <param name="in" value="ProteinQuantifier_input.consensusXML"/>
       <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="mztab" file="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
       <param name="top" value="3"/>
       <param name="average" value="sum"/>
       <param name="include_all" value="true"/>
@@ -23832,7 +24686,7 @@
         <param name="quoting" value="double"/>
         <param name="replacement" value="_"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mztab_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -24047,9 +24901,9 @@
         <param name="tolerance" value="20.0"/>
       </section>
       <section name="MS2_id_rate">
-        <param name="force_no_fdr" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_cm_FLAG"/>
+        <param name="assume_all_target" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_cm_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -24570,6 +25424,7 @@
       <output name="out" file="SimpleSearchEngine_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
       <section name="Search">
         <param name="enzyme" value="Trypsin"/>
+        <param name="decoys" value="false"/>
         <section name="precursor">
           <param name="mass_tolerance" value="5.0"/>
           <param name="mass_tolerance_unit" value="ppm"/>
@@ -24586,6 +25441,9 @@
           <param name="variable" value="Oxidation (M)"/>
           <param name="variable_max_per_peptide" value="2"/>
         </section>
+        <section name="annotate">
+          <param name="PSM" value=""/>
+        </section>
         <section name="peptide">
           <param name="min_size" value="7"/>
           <param name="max_size" value="40"/>
@@ -24635,7 +25493,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="true"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -24679,7 +25536,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="true"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -24723,7 +25579,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="true"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -24767,7 +25622,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -24811,7 +25665,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -24855,7 +25708,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="false"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -24892,7 +25744,7 @@
       <section name="sirius">
         <param name="profile" value="qtof"/>
         <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
+        <param name="database" value="pubchem"/>
         <param name="noise" value="0"/>
         <param name="ppm_max" value="10"/>
         <param name="isotope" value="both"/>
@@ -24900,7 +25752,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="true"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -25035,6 +25886,8 @@
   <xml name="autotest_SpectraMerger">
 </xml>
   <xml name="autotest_SpectraSTSearchAdapter"/>
+  <xml name="autotest_StaticModification">
+</xml>
   <xml name="autotest_SvmTheoreticalSpectrumGeneratorTrainer">
 </xml>
   <xml name="autotest_TargetedFileConverter">
@@ -25487,7 +26340,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_1_input.featureXML"/>
-      <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25510,7 +26363,7 @@
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25524,7 +26377,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_2_input.consensusXML"/>
-      <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25550,7 +26403,7 @@
       <output name="consensus_centroids" file="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta="5700" ftype="csv"/>
       <output name="consensus_elements" file="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta="5700" ftype="csv"/>
       <output name="consensus_features" file="TextExporter_2_consensus_features.tmp" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25564,7 +26417,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_3_input.idXML"/>
-      <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25587,7 +26440,7 @@
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25601,7 +26454,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_3_input.idXML"/>
-      <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25624,7 +26477,7 @@
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25638,7 +26491,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_5_input.idXML"/>
-      <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25661,7 +26514,7 @@
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25675,7 +26528,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_6_input.featureXML"/>
-      <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25698,7 +26551,7 @@
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25712,7 +26565,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_7_input.consensusXML"/>
-      <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25735,7 +26588,7 @@
         <param name="sort_by_maps" value="true"/>
         <param name="sort_by_size" value="true"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25749,7 +26602,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_1_input.featureXML"/>
-      <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25772,7 +26625,7 @@
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25786,7 +26639,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_9_input.idXML"/>
-      <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25809,7 +26662,7 @@
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25909,8 +26762,8 @@
       <param name="in" value="TOFCalibration_1_input.mzML"/>
       <output name="out" file="TOFCalibration_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
       <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/>
-      <param name="ref_masses" value="TOFCalibration_ref_masses.txt" ftype="txt"/>
-      <param name="tof_const" value="TOFCalibration_const.csv" ftype="csv"/>
+      <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
+      <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
       <param name="peak_data" value="false"/>
       <section name="algorithm">
         <section name="PeakPicker">
@@ -25991,8 +26844,8 @@
       <param name="in" value="TOFCalibration_2_input.mzML"/>
       <output name="out" file="TOFCalibration_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
       <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/>
-      <param name="ref_masses" value="TOFCalibration_ref_masses.txt" ftype="txt"/>
-      <param name="tof_const" value="TOFCalibration_const.csv" ftype="csv"/>
+      <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
+      <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
       <param name="peak_data" value="true"/>
       <section name="algorithm">
         <section name="PeakPicker">
@@ -26316,5 +27169,37 @@
         </assert_contents>
       </output>
     </test>
-  </xml>
-<xml name="autotest_InspectAdapter"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_RTPredict"/><xml name="autotest_OpenSwathDIAPreScoring"/><xml name="autotest_DigestorMotif"/><xml name="autotest_PTPredict"/></macros>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="spectra.mzML"/>
+      <output name="out" file="XTandemAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="database" value="proteinslong.fasta"/>
+      <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/>
+      <param name="ignore_adapter_param" value="false"/>
+      <param name="precursor_mass_tolerance" value="5.0"/>
+      <param name="fragment_mass_tolerance" value="0.3"/>
+      <param name="precursor_error_units" value="ppm"/>
+      <param name="fragment_error_units" value="Da"/>
+      <param name="max_precursor_charge" value="0"/>
+      <param name="no_isotope_error" value="false"/>
+      <param name="fixed_modifications" value=""/>
+      <param name="variable_modifications" value="Oxidation (M)"/>
+      <param name="minimum_fragment_mz" value="150.0"/>
+      <param name="enzyme" value="Trypsin"/>
+      <param name="missed_cleavages" value="1"/>
+      <param name="semi_cleavage" value="false"/>
+      <param name="output_results" value="all"/>
+      <param name="max_valid_expect" value="0.1"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+  </xml>
+<xml name="autotest_PTPredict"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_RTPredict"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_InspectAdapter"/></macros>
diff -r 24a506151bdf -r 5aabc469cce0 macros_test.xml
--- a/macros_test.xml	Thu Sep 24 09:54:05 2020 +0000
+++ b/macros_test.xml	Tue Oct 13 19:58:04 2020 +0000
@@ -177,20 +177,7 @@
     <output name="out" ftype="txt" value="MapStatistics2.txt"/>
   </test>
 </xml>
-<xml name="manutest_MetaboliteAdductDecharger">
-  <test expect_num_outputs="3"><!-- same input as used by Decharger -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="featurexml" value="Decharger_input.featureXML"/>
-    <output name="out_cm" ftype="consensusxml" value="MetaboliteAdductDecharger_cm.consensusXML" compare="sim_size"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_fm_FLAG,outpairs_FLAG"/>
-    <output name="out_fm" ftype="featurexml" value="MetaboliteAdductDecharger_fm.featureXML" compare="sim_size"/>
-    <output name="outpairs" ftype="consensusxml" value="MetaboliteAdductDecharger_pairs.consensusXML" compare="sim_size"/>
-  </test>
-</xml>
 <xml name="manutest_MetaboliteSpectralMatcher">
-    <!-- https://github.com/OpenMS/OpenMS/issues/2078 
-        https://github.com/OpenMS/OpenMS/pull/4468-->
     <!-- same input as used in the MSGF+Adapter, should use database CHEMISTRY/MetaboliteSpectralDB.mzML -->
   <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter, used as input and database -->
     <param name="adv_opts_selector" value="advanced"/>
@@ -274,36 +261,46 @@
 </test>
 </xml>
 <xml name="manutest_OpenSwathDIAPreScoring">
-  <!-- TODO data from a test that included all the needed test files 
-       currently unusable https://github.com/OpenMS/OpenMS/pull/4443 -->
   <!-- data from a test that included all the needed test files -->
-<!--  <test>-->
-<!--    <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>-->
-<!--    <param name="swath_files" value="OpenSwathWorkflow_10.chrom.mzML.tmp"/> or OpenSwathAnalyzer_2_swathfile.mzML-->
-<!--    <output name="out" ftype="tabular" value="OpenSwathDIAPreScoring_2.tmp"/>-->
-<!--  </test>-->
+  <test>
+    <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
+    <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
+    <output_collection name="output_files" count="1">
+      <element name="OpenSwathAnalyzer_2_swathfile_mzML.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
+    </output_collection>
+  </test>
+  
+  <!-- test with two inputs (actually the same file .. symlinked) -->
+  <test>
+    <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
+    <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/>
+    <output_collection name="output_files" count="2">
+      <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
+      <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
+    </output_collection>
+  </test>
 </xml>
 <!-- adapted from macros_discarded_auto.xml (due to prefix-output)-->
 <xml name="manutest_OpenSwathFileSplitter">
-<test expect_num_outputs="3">
-  <conditional name="adv_opts_cond">
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="force" value="false"/>
-    <param name="test" value="true"/>
-  </conditional>
-  <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-  <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/>
-  <output_collection name="outputDirectory" count="6">
-    <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/>
-    <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/>
-  </output_collection>
-  <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>
-  <output name="ctd_out" ftype="xml">
-    <assert_contents>
-      <is_valid_xml/>
-    </assert_contents>
-  </output>
-</test>
+  <test expect_num_outputs="3">
+    <conditional name="adv_opts_cond">
+      <param name="adv_opts_selector" value="advanced"/>
+      <param name="force" value="false"/>
+      <param name="test" value="true"/>
+    </conditional>
+    <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
+    <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/>
+    <output_collection name="outputDirectory" count="6">
+      <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/>
+      <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/>
+    </output_collection>
+    <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>
+    <output name="ctd_out" ftype="xml">
+      <assert_contents>
+        <is_valid_xml/>
+      </assert_contents>
+    </output>
+  </test>
 </xml>
 <xml name="manutest_OpenSwathRewriteToFeatureXML">
   <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
@@ -346,7 +343,7 @@
     <param name="adv_opts_cond|adv_opts_selector" value="advanced"/>
     <param name="adv_opts_cond|skip_db_check" value="true"/>
     <param name="out_type" value="idxml"/>
-    <output name="out" ftype="idxml" value="PSMFeatureExtractor.idxml" compare="sim_size" delta="100"/>
+    <output name="out" ftype="idxml" value="PSMFeatureExtractor.idxml" compare="sim_size" delta="500"/>
   </test>
   <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
     <param name="adv_opts_cond|test" value="true"/>
@@ -355,7 +352,7 @@
     <param name="adv_opts_cond|adv_opts_selector" value="advanced"/>
     <param name="adv_opts_cond|skip_db_check" value="true"/>
     <param name="out_type" value="mzid"/>
-    <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="100" lines_diff="4"/>
+    <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="500"/>
   </test>
 </xml>
 <xml name="manutest_QCCalculator">
@@ -429,12 +426,11 @@
 </xml>
 <xml name="manutest_RTEvaluation">
   <!-- just chosen an arbitrary input and autgenerated output-->
-  <!-- https://github.com/OpenMS/OpenMS/pull/4429 -->
   <test expect_num_outputs="1">
     <param name="adv_opts_selector" value="advanced"/>
     <param name="adv_opts_cond|test" value="true"/>
     <param name="in" ftype="idxml" value="PeptideIndexer_1.idXML"/>
-    <output name="out" ftype="csv" value="RTEvaluation.tsv"/>
+    <output name="out" ftype="tabular" value="RTEvaluation.tsv"/>
   </test>
 </xml>
 <xml name="manutest_SemanticValidator">
@@ -546,4 +542,4 @@
     </output>
   </test>
 </xml>
-<xml name="manutest_IDMapper"/><xml name="manutest_ProteinQuantifier"/><xml name="manutest_PeakPickerIterative"/><xml name="manutest_FeatureLinkerUnlabeledQT"/><xml name="manutest_TICCalculator"/><xml name="manutest_IDFilter"/><xml name="manutest_IDPosteriorErrorProbability"/><xml name="manutest_FeatureFinderIdentification"/><xml name="manutest_XFDR"/><xml name="manutest_OpenSwathWorkflow"/><xml name="manutest_MassCalculator"/><xml name="manutest_IDFileConverter"/><xml name="manutest_MultiplexResolver"/><xml name="manutest_FeatureFinderSuperHirn"/><xml name="manutest_AssayGeneratorMetabo"/><xml name="manutest_MassTraceExtractor"/><xml name="manutest_SiriusAdapter"/><xml name="manutest_IDMerger"/><xml name="manutest_MSstatsConverter"/><xml name="manutest_FileMerger"/><xml name="manutest_Decharger"/><xml name="manutest_PTPredict"/><xml name="manutest_XTandemAdapter"/><xml name="manutest_FeatureFinderMetabo"/><xml name="manutest_CruxAdapter"/><xml name="manutest_OpenSwathConfidenceScoring"/><xml name="manutest_PrecursorIonSelector"/><xml name="manutest_ConsensusMapNormalizer"/><xml name="manutest_RTPredict"/><xml name="manutest_PercolatorAdapter"/><xml name="manutest_ProteinInference"/><xml name="manutest_OpenSwathDecoyGenerator"/><xml name="manutest_TextExporter"/><xml name="manutest_FeatureFinderCentroided"/><xml name="manutest_DecoyDatabase"/><xml name="manutest_SpectraFilterWindowMower"/><xml name="manutest_NoiseFilterGaussian"/><xml name="manutest_MaRaClusterAdapter"/><xml name="manutest_ConsensusID"/><xml name="manutest_FileFilter"/><xml name="manutest_InclusionExclusionListCreator"/><xml name="manutest_FeatureLinkerUnlabeledKD"/><xml name="manutest_NovorAdapter"/><xml name="manutest_OpenPepXL"/><xml name="manutest_SeedListGenerator"/><xml name="manutest_FalseDiscoveryRate"/><xml name="manutest_OpenPepXLLF"/><xml name="manutest_SpecLibSearcher"/><xml name="manutest_IDConflictResolver"/><xml name="manutest_MRMMapper"/><xml name="manutest_OMSSAAdapter"/><xml name="manutest_ExternalCalibration"/><xml name="manutest_PeakPickerHiRes"/><xml name="manutest_MascotAdapter"/><xml name="manutest_FeatureFinderMultiplex"/><xml name="manutest_MetaProSIP"/><xml name="manutest_FuzzyDiff"/><xml name="manutest_TargetedFileConverter"/><xml name="manutest_MapAlignerIdentification"/><xml name="manutest_IDRTCalibration"/><xml name="manutest_MRMTransitionGroupPicker"/><xml name="manutest_RTModel"/><xml name="manutest_OpenSwathAssayGenerator"/><xml name="manutest_IDSplitter"/><xml name="manutest_OpenSwathMzMLFileCacher"/><xml name="manutest_HighResPrecursorMassCorrector"/><xml name="manutest_OpenSwathChromatogramExtractor"/><xml name="manutest_OpenSwathAnalyzer"/><xml name="manutest_FeatureLinkerUnlabeled"/><xml name="manutest_CompNovoCID"/><xml name="manutest_DTAExtractor"/><xml name="manutest_FileInfo"/><xml name="manutest_MapAlignerSpectrum"/><xml name="manutest_IsobaricAnalyzer"/><xml name="manutest_LowMemPeakPickerHiRes"/><xml name="manutest_MyriMatchAdapter"/><xml name="manutest_InternalCalibration"/><xml name="manutest_TOFCalibration"/><xml name="manutest_MSGFPlusAdapter"/><xml name="manutest_PTModel"/><xml name="manutest_InspectAdapter"/><xml name="manutest_SpectraFilterSqrtMower"/><xml name="manutest_SimpleSearchEngine"/><xml name="manutest_PeakPickerWavelet"/><xml name="manutest_MapNormalizer"/><xml name="manutest_IDScoreSwitcher"/><xml name="manutest_FeatureLinkerLabeled"/><xml name="manutest_MapRTTransformer"/><xml name="manutest_RNPxlSearch"/><xml name="manutest_PrecursorMassCorrector"/><xml name="manutest_MapAlignerPoseClustering"/><xml name="manutest_MzTabExporter"/><xml name="manutest_BaselineFilter"/><xml name="manutest_FeatureFinderMRM"/><xml name="manutest_MascotAdapterOnline"/><xml name="manutest_DatabaseFilter"/><xml name="manutest_ProteinResolver"/><xml name="manutest_OpenSwathFeatureXMLToTSV"/><xml name="manutest_FidoAdapter"/><xml name="manutest_AccurateMassSearch"/><xml name="manutest_CompNovo"/><xml name="manutest_LowMemPeakPickerHiResRandomAccess"/><xml name="manutest_OpenSwathRTNormalizer"/><xml name="manutest_PeptideIndexer"/><xml name="manutest_CometAdapter"/><xml name="manutest_NoiseFilterSGolay"/><xml name="manutest_MSFraggerAdapter"/><xml name="manutest_SpectraSTSearchAdapter"/><xml name="manutest_SequestAdapter"/><xml name="manutest_FeatureFinder"/><xml name="manutest_LuciphorAdapter"/><xml name="manutest_GNPSExport"/><xml name="manutest_Epifany"/><xml name="manutest_NucleicAcidSearchEngine"/><xml name="manutest_QualityControl"/><xml name="manutest_FeatureFinderMetaboIdent"/><xml name="manutest_RNAMassCalculator"/><xml name="manutest_MapAlignerTreeGuided"/><xml name="manutest_IDMassAccuracy"/><xml name="manutest_ProteomicsLFQ"/><xml name="manutest_IDDecoyProbability"/><xml name="manutest_DigestorMotif"/></macros>
+<xml name="manutest_MetaboliteAdductDecharger"/><xml name="manutest_IDMapper"/><xml name="manutest_ProteinQuantifier"/><xml name="manutest_PeakPickerIterative"/><xml name="manutest_FeatureLinkerUnlabeledQT"/><xml name="manutest_TICCalculator"/><xml name="manutest_IDFilter"/><xml name="manutest_IDPosteriorErrorProbability"/><xml name="manutest_FeatureFinderIdentification"/><xml name="manutest_XFDR"/><xml name="manutest_OpenSwathWorkflow"/><xml name="manutest_MassCalculator"/><xml name="manutest_IDFileConverter"/><xml name="manutest_MultiplexResolver"/><xml name="manutest_FeatureFinderSuperHirn"/><xml name="manutest_AssayGeneratorMetabo"/><xml name="manutest_MassTraceExtractor"/><xml name="manutest_SiriusAdapter"/><xml name="manutest_IDMerger"/><xml name="manutest_MSstatsConverter"/><xml name="manutest_FileMerger"/><xml name="manutest_Decharger"/><xml name="manutest_PTPredict"/><xml name="manutest_XTandemAdapter"/><xml name="manutest_FeatureFinderMetabo"/><xml name="manutest_CruxAdapter"/><xml name="manutest_OpenSwathConfidenceScoring"/><xml name="manutest_PrecursorIonSelector"/><xml name="manutest_ConsensusMapNormalizer"/><xml name="manutest_RTPredict"/><xml name="manutest_PercolatorAdapter"/><xml name="manutest_ProteinInference"/><xml name="manutest_OpenSwathDecoyGenerator"/><xml name="manutest_TextExporter"/><xml name="manutest_FeatureFinderCentroided"/><xml name="manutest_DecoyDatabase"/><xml name="manutest_SpectraFilterWindowMower"/><xml name="manutest_NoiseFilterGaussian"/><xml name="manutest_MaRaClusterAdapter"/><xml name="manutest_ConsensusID"/><xml name="manutest_FileFilter"/><xml name="manutest_InclusionExclusionListCreator"/><xml name="manutest_FeatureLinkerUnlabeledKD"/><xml name="manutest_NovorAdapter"/><xml name="manutest_OpenPepXL"/><xml name="manutest_SeedListGenerator"/><xml name="manutest_FalseDiscoveryRate"/><xml name="manutest_OpenPepXLLF"/><xml name="manutest_SpecLibSearcher"/><xml name="manutest_IDConflictResolver"/><xml name="manutest_MRMMapper"/><xml name="manutest_OMSSAAdapter"/><xml name="manutest_ExternalCalibration"/><xml name="manutest_PeakPickerHiRes"/><xml name="manutest_MascotAdapter"/><xml name="manutest_FeatureFinderMultiplex"/><xml name="manutest_MetaProSIP"/><xml name="manutest_FuzzyDiff"/><xml name="manutest_TargetedFileConverter"/><xml name="manutest_MapAlignerIdentification"/><xml name="manutest_IDRTCalibration"/><xml name="manutest_MRMTransitionGroupPicker"/><xml name="manutest_RTModel"/><xml name="manutest_OpenSwathAssayGenerator"/><xml name="manutest_IDSplitter"/><xml name="manutest_OpenSwathMzMLFileCacher"/><xml name="manutest_HighResPrecursorMassCorrector"/><xml name="manutest_OpenSwathChromatogramExtractor"/><xml name="manutest_OpenSwathAnalyzer"/><xml name="manutest_FeatureLinkerUnlabeled"/><xml name="manutest_CompNovoCID"/><xml name="manutest_DTAExtractor"/><xml name="manutest_FileInfo"/><xml name="manutest_MapAlignerSpectrum"/><xml name="manutest_IsobaricAnalyzer"/><xml name="manutest_LowMemPeakPickerHiRes"/><xml name="manutest_MyriMatchAdapter"/><xml name="manutest_InternalCalibration"/><xml name="manutest_TOFCalibration"/><xml name="manutest_MSGFPlusAdapter"/><xml name="manutest_PTModel"/><xml name="manutest_InspectAdapter"/><xml name="manutest_SpectraFilterSqrtMower"/><xml name="manutest_SimpleSearchEngine"/><xml name="manutest_PeakPickerWavelet"/><xml name="manutest_MapNormalizer"/><xml name="manutest_IDScoreSwitcher"/><xml name="manutest_FeatureLinkerLabeled"/><xml name="manutest_MapRTTransformer"/><xml name="manutest_RNPxlSearch"/><xml name="manutest_PrecursorMassCorrector"/><xml name="manutest_MapAlignerPoseClustering"/><xml name="manutest_MzTabExporter"/><xml name="manutest_BaselineFilter"/><xml name="manutest_FeatureFinderMRM"/><xml name="manutest_MascotAdapterOnline"/><xml name="manutest_DatabaseFilter"/><xml name="manutest_ProteinResolver"/><xml name="manutest_OpenSwathFeatureXMLToTSV"/><xml name="manutest_FidoAdapter"/><xml name="manutest_AccurateMassSearch"/><xml name="manutest_CompNovo"/><xml name="manutest_LowMemPeakPickerHiResRandomAccess"/><xml name="manutest_OpenSwathRTNormalizer"/><xml name="manutest_PeptideIndexer"/><xml name="manutest_CometAdapter"/><xml name="manutest_NoiseFilterSGolay"/><xml name="manutest_MSFraggerAdapter"/><xml name="manutest_SpectraSTSearchAdapter"/><xml name="manutest_SequestAdapter"/><xml name="manutest_FeatureFinder"/><xml name="manutest_LuciphorAdapter"/><xml name="manutest_GNPSExport"/><xml name="manutest_Epifany"/><xml name="manutest_NucleicAcidSearchEngine"/><xml name="manutest_QualityControl"/><xml name="manutest_FeatureFinderMetaboIdent"/><xml name="manutest_RNAMassCalculator"/><xml name="manutest_MapAlignerTreeGuided"/><xml name="manutest_IDMassAccuracy"/><xml name="manutest_ProteomicsLFQ"/><xml name="manutest_IDDecoyProbability"/><xml name="manutest_DigestorMotif"/><xml name="manutest_DatabaseSuitability"/><xml name="manutest_StaticModification"/></macros>
diff -r 24a506151bdf -r 5aabc469cce0 prepare_test_data.sh
--- a/prepare_test_data.sh	Thu Sep 24 09:54:05 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1196 +0,0 @@
-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 24a506151bdf -r 5aabc469cce0 prepare_test_data_manual.sh
--- a/prepare_test_data_manual.sh	Thu Sep 24 09:54:05 2020 +0000
+++ b/prepare_test_data_manual.sh	Tue Oct 13 19:58:04 2020 +0000
@@ -55,7 +55,15 @@
 
 # TODO MRMPairFinder
 
-# TODO OpenSwathDIAPreScoring
+# generate two inputs for OpenSwathDIAPreScoring
+OpenSwathDIAPreScoring -tr OpenSwathWorkflow_1_input.TraML -swath_files OpenSwathAnalyzer_2_swathfile.mzML -output_files OpenSwathDIAPreScoring.tsv > OpenSwathDIAPreScoring.stdout 2> stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'OpenSwathDIAPreScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
+
+# generate two inputs for OpenSwathDIAPreScoring by linking
+ln -s OpenSwathAnalyzer_2_swathfile.mzML OpenSwathDIAPreScoring_in1.mzML
+ln -s OpenSwathAnalyzer_2_swathfile.mzML OpenSwathDIAPreScoring_in2.mzML
+OpenSwathDIAPreScoring -tr OpenSwathWorkflow_1_input.TraML -swath_files OpenSwathDIAPreScoring_in1.mzML OpenSwathDIAPreScoring_in2.mzML -output_files OpenSwathDIAPreScoring_2_1.tsv OpenSwathDIAPreScoring_2_2.tsv > OpenSwathDIAPreScoring.stdout 2> stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'OpenSwathDIAPreScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
 OpenSwathRewriteToFeatureXML -featureXML OpenSwathFeatureXMLToTSV_input.featureXML -out OpenSwathRewriteToFeatureXML.featureXML > OpenSwathRewriteToFeatureXML.stdout 2> stderr
 # if [[ "$?" -ne "0" ]]; then >&2 echo 'OpenSwathRewriteToFeatureXML failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
@@ -107,10 +115,8 @@
 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
+RTEvaluation -in PeptideIndexer_1.idXML -out RTEvaluation.tsv > RTEvaluation.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'RTEvaluation failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-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
diff -r 24a506151bdf -r 5aabc469cce0 test-data.sh
--- a/test-data.sh	Thu Sep 24 09:54:05 2020 +0000
+++ b/test-data.sh	Tue Oct 13 19:58:04 2020 +0000
@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-VERSION=2.5
+VERSION=2.6
 FILETYPES="filetypes.txt"
-CONDAPKG="https://anaconda.org/bioconda/openms/2.5.0/download/linux-64/openms-2.5.0-h463af6b_1.tar.bz2"
+CONDAPKG="https://anaconda.org/bioconda/openms/2.6.0/download/linux-64/openms-2.6.0-h4afb90d_0.tar.bz2"
 
 # import the magic
 . ./generate-foo.sh
@@ -49,7 +49,7 @@
 	cd -
 else
 	cd $OPENMSGIT
-		git pull origin release/$VERSION.0
+	git pull origin release/$VERSION.0
 	cd -
 fi
 
@@ -59,7 +59,7 @@
 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
+	conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -p $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION ctdopts=1.4 lxml
 # chmod -R u-w $OPENMSENV 
 fi
 ###############################################################################
@@ -88,7 +88,6 @@
 	git pull origin topic/cdata
 	cd -
 fi
-# export PYTHONPATH=$(pwd)/CTDopts
 
 ###############################################################################
 ## copy all the test data files to test-data
@@ -103,21 +102,26 @@
 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/
+	wget -nc https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML
+	mv MetaboliteSpectralDB.mzML test-data/
 fi
 ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt
 ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv
 
 if [ ! -d test-data/pepnovo_models/ ]; then
-	wget http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip
-	unzip -e PepNovo.20120423.zip -d /tmp/
-	mv /tmp/Models test-data/pepnovo_models/
+	mkdir -p /tmp/pepnovo
+	wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip
+	unzip PepNovo.20120423.zip -d /tmp/pepnovo/
+	mv /tmp/pepnovo/Models test-data/pepnovo_models/
+	rm PepNovo.20120423.zip
+	rm -rf /tmp/pepnovo
 fi
 ###############################################################################
 ## generate ctd files using the binaries in the conda package 
 ###############################################################################
 echo "Create CTD files"
 conda activate $OPENMSENV
+rm -rf ctd
 mkdir -p ctd
 
 # TODO because of https://github.com/OpenMS/OpenMS/issues/4641
@@ -175,7 +179,7 @@
 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 SPECTRAST_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/SpectraST/spectrast"' >> prepare_test_data.sh
 echo 'export XTANDEM_BINARY="xtandem"' >> prepare_test_data.sh
 echo 'export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"' >> prepare_test_data.sh
 
diff -r 24a506151bdf -r 5aabc469cce0 tools_blacklist.txt
--- a/tools_blacklist.txt	Thu Sep 24 09:54:05 2020 +0000
+++ b/tools_blacklist.txt	Tue Oct 13 19:58:04 2020 +0000
@@ -1,5 +1,5 @@
 # seems not possible for 2.5 https://github.com/OpenMS/OpenMS/issues/4426
-DigestorMotif
+# 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
@@ -12,9 +12,6 @@
 # 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