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Changeset 6:9a6e3bb0f358 (2020-10-13)

Previous changeset 5:e38e1a7af019 (2020-09-23) Next changeset 7:4fdeb75928ea (2020-11-06)

Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"

modified:
404-urls.patch
XFDR.xml
filetypes.txt
generate-foo.sh
generate.sh
hardcoded_params.json
macros.xml
macros_autotest.xml
macros_test.xml
prepare_test_data_manual.sh
test-data.sh
tools_blacklist.txt

removed:
prepare_test_data.sh

diff -r e38e1a7af019 -r 9a6e3bb0f358 404-urls.patch
--- a/404-urls.patch Wed Sep 23 14:59:36 2020 +0000
+++ b/404-urls.patch Tue Oct 13 20:38:11 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 e38e1a7af019 -r 9a6e3bb0f358 XFDR.xml
--- a/XFDR.xml Wed Sep 23 14:59:36 2020 +0000
+++ b/XFDR.xml Tue Oct 13 20:38:11 2020 +0000

[

@@ -87,15 +87,15 @@
     <param name="minscore" argument="-minscore" type="float" optional="true" value="-10.0" label="Minimum score to be considered for FDR calculation" help="A number lower than the lowest score will effectively disable this filter"/>
     <param name="binsize" argument="-binsize" type="float" optional="true" min="1e-15" value="0.0001" label="Bin size for the cumulative histograms for score distributions" help="Should be about the same size as the smallest expected difference between scores. Smaller numbers will make XFDR more robust, but much slower. Negative numbers are not allowed. Should only be changed if the range of the main score changes or another score than the OpenPepXL score is used"/>
     <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="false">
-      <option value="out_idXML_FLAG">out_idXML (Enables the test mode (needed for internal use only))</option>
-      <option value="out_mzIdentML_FLAG">out_mzIdentML (Enables the test mode (needed for internal use only))</option>
-      <option value="out_xquest_FLAG">out_xquest (Enables the test mode (needed for internal use only))</option>
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="out_idXML_FLAG">out_idXML (Output as idXML file)</option>
+      <option value="out_mzIdentML_FLAG">out_mzIdentML (Output as mzIdentML file)</option>
+      <option value="out_xquest_FLAG">out_xquest (Output as xquest.xml file)</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
@@ -123,6 +123,6 @@
   <help><![CDATA[Calculates false discovery rate estimates on crosslink identifications

-For more information, visit http://www.openms.de/documentation/TOPP_XFDR.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_XFDR.html]]></help>
   <expand macro="references"/>
</tool>

diff -r e38e1a7af019 -r 9a6e3bb0f358 filetypes.txt
--- a/filetypes.txt Wed Sep 23 14:59:36 2020 +0000
+++ b/filetypes.txt Tue Oct 13 20:38:11 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 e38e1a7af019 -r 9a6e3bb0f358 generate-foo.sh
--- a/generate-foo.sh Wed Sep 23 14:59:36 2020 +0000
+++ b/generate-foo.sh Tue Oct 13 20:38:11 2020 +0000

[

b'@@ -2,125 +2,126 @@\n \n # parse test definitions from OpenMS sources for a tool with a given id\n function get_tests2 {\n-\tid=$1\n-\t>&2 echo "generate tests for $id"\n-\techo \'<xml name="autotest_\'"$id"\'">\'\n+ id=$1\n+ >&2 echo "generate tests for $id"\n+ echo \'<xml name="autotest_\'"$id"\'">\'\n \n-\t# get the tests from the CMakeLists.txt\n-\t# 1st remove some tests\n-\t# - Filefilter with empty select_palarity value (empty is not in the list of allowed options)\n-\t# - MassTraceExtractor with outdated ini file leading to wrong parameters https://github.com/OpenMS/OpenMS/issues/4386\n-\t# - OpenSwathMzMLFileCacher with -convert_back argumen https://github.com/OpenMS/OpenMS/issues/4399\n+ # get the tests from the CMakeLists.txt\n+ # 1st remove some tests\n+ # - OpenSwathMzMLFileCacher with -convert_back argumen https://github.com/OpenMS/OpenMS/issues/4399\n # - IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differentlt\n-\t# - several tools with duplicated input (leads to conflict when linking)\n-\t# - TOFCalibration inputs we extension (also in prepare_test_data) https://github.com/OpenMS/OpenMS/pull/4525\n-\t# - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456)\n-\t# - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed)\n-\t# - some input files are originally in a subdir (degenerated cases/), but not in test-data\n-\t# - SeedListGenerator: https://github.com/OpenMS/OpenMS/issues/4404\n-\t# - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet)\n-\tCMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake |\n-\t\tsed \'s@${DATA_DIR_SHARE}/@@g\' |\n-\t\tgrep -v \'OpenSwathMzMLFileCacher .*-convert_back\' |\n-\t \tsed \'s/${TMP_RIP_PATH}/""/\' |\n-\t\tsed \'s@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @\' |\n-\t\tgrep -v "MaRaClusterAdapter.*-consensus_out"|\n- \t\tgrep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " |\n-\t\tsed \'s@degenerate_cases/@@g\' |\n-\t\tgrep -v \'TOPP_SeedListGenerator_3"\' | \n-\t\tegrep -v \'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"\')\n+ # - several tools with duplicated input (leads to conflict when linking)\n+ # - TOFCalibration inputs we extension (also in prepare_test_data) https://github.com/OpenMS/OpenMS/pull/4525\n+ # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456)\n+ # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed)\n+ # - some input files are originally in a subdir (degenerated cases/), but not in test-data\n+ # - SeedListGenerator: https://github.com/OpenMS/OpenMS/issues/4404\n+ # - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet)\n+ # - FeatureFinderIdentification name clash of two tests https://github.com/OpenMS/OpenMS/pull/5002\n+ # - TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010\n+ CMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake |\n+ sed \'s@${DATA_DIR_SHARE}/@@g\' |\n+ grep -v \'OpenSwathMzMLFileCacher .*-convert_back\' |\n+ sed \'s/${TMP_RIP_PATH}/""/\' |\n+ grep -v "MaRaClusterAdapter.*-consensus_out"|\n+ grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " |\n+ sed \'s@degenerate_cases/@@g\' |\n+ grep -v \'TOPP_SeedListGenerator_3"\' | \n+ egrep -v \'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"\' |\n+\tegrep -v \'"TOPP_FeatureFinderIdentification_4"\' | \n+\tsed \'s/\$"TOPP_SiriusAdapter_4".*\$-sirius:database all\$.*\$/\\1-sirius:database pubchem\\2/\')\n \n \n-# \t\tgrep -v \'FileFilter.*-spectra:select_polarity ""\' |\n-# \t\tgrep -v \'MassTraceExtractor_2.ini \' |\n-# \t\tgrep -v "FileMerger_6_input2.mzML.*FileMerger_6_input2.mzML" |\n-# \t\tgrep -v "IDMerger_1_input1.idXML.*IDMerger_1'..b'p \'\\${DIFF}.*\'"$a")\n+# >&2 echo " g "$g\n+ in1=$(sed \'s/.*-in1 \$[^ ]\\+\$.*/\\1/\' <<<$g)\n+ # >&2 echo " in1 "$in1\n+ if [[ "$a" != "$in1" ]]; then\n+ ret="$ret $a"\n+ continue\n+ fi\n+ in2=$(sed \'s/.*-in2 \$[^ ]\\+\$.*/\\1/\' <<<$g)\n+ in2=$(basename $in2 | sed \'s/)$//\')\n+ # >&2 echo " in2 "$in2\n+ if [[ -f "test-data/$in2" ]]; then\n+ ln -fs "$in1" "test-data/$in2"\n+ ret="$ret $in2"\n+ else\n+ ret="$ret $a"\n+ fi\n+ done\n+# >&2 echo "--> $ret"\n+ echo "$ret"\n }\n \n function link_tmp_files {\n@@ -190,28 +191,32 @@\n \n # parse data preparation calls from OpenMS sources for a tool with a given id\n function prepare_test_data {\n-# \tid=$1\n+# id=$1\n # | egrep -i "$id\\_.*[0-9]+(_prepare\\"|_convert)?"\n-\tcat $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@", $0)}\' | sed \'s/)@NEWLINE@/)\\n/g\' | sed \'s/@NEWLINE@/ /g\' | \n-\t\tsed \'s/degenerate_cases\\///\' | \n-\t\tegrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | \n-\t\tgrep add_test | \n-\t\tegrep "TOPP|UTILS" |\n-\t\tsed \'s@${DATA_DIR_SHARE}/@@g;\'|\n-\t\tsed \'s@${TMP_RIP_PATH}@dummy2.tmp@g\'|\n-\t\tsed \'s@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @\'| \n-\twhile read line\n-\tdo\n-\t\ttest_id=$(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)\n \n-\t\tif grep -lq "$test_id"\'\\".* PROPERTIES WILL_FAIL 1\' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then\n-\t\t\t>&2 echo " skip failing "$test_id\n-\t\t\tcontinue\n-\t\tfi\n+# TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010\n+ 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@", $0)}\' | sed \'s/)@NEWLINE@/)\\n/g\' | sed \'s/@NEWLINE@/ /g\' | \n+ sed \'s/degenerate_cases\\///\' | \n+ egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | \n+ grep add_test | \n+ egrep "TOPP|UTILS" |\n+ sed \'s@${DATA_DIR_SHARE}/@@g;\'|\n+ sed \'s@${TMP_RIP_PATH}@dummy2.tmp@g\'|\n+ sed \'s@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @\'| \n+\tsed \'s/\$"TOPP_SiriusAdapter_4".*\$-sirius:database all\$.*\$/\\1-sirius:database pubchem\\2/\' |\n+ while read line\n+ do\n+ test_id=$(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)\n \n-\t\tline=$(echo "$line" | sed \'s/add_test("//; s/)[^)]*$//; s/\\${TOPP_BIN_PATH}\\///g;s/\\${DATA_DIR_TOPP}\\///g; s#THIRDPARTY/##g\' | cut -d" " -f2-)\n-\t\t# line="$(fix_tmp_files $line)"\n-\t\techo "$line > $test_id.stdout 2> $test_id.stderr"\n-\t\techo "if [[ \\"\\$?\\" -ne \\"0\\" ]]; then >&2 echo \'$test_id failed\'; >&2 echo -e \\"stderr:\\n\\$(cat $test_id.stderr | sed \'s/^/ /\')\\"; echo -e \\"stdout:\\n\\$(cat $test_id.stdout)\\";fi"\t\n+ if grep -lq "$test_id"\'\\".* PROPERTIES WILL_FAIL 1\' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then\n+ >&2 echo " skip failing "$test_id\n+ continue\n+ fi\n+\n+ line=$(echo "$line" | sed \'s/add_test("//; s/)[^)]*$//; s/\\${TOPP_BIN_PATH}\\///g;s/\\${DATA_DIR_TOPP}\\///g; s#THIRDPARTY/##g\' | cut -d" " -f2-)\n+ # line="$(fix_tmp_files $line)"\n+ echo \'echo executing "\'$test_id\'"\'\n+\techo "$line > $test_id.stdout 2> $test_id.stderr"\n+ echo "if [[ \\"\\$?\\" -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" \n done\n }\n'

diff -r e38e1a7af019 -r 9a6e3bb0f358 generate.sh
--- a/generate.sh Wed Sep 23 14:59:36 2020 +0000
+++ b/generate.sh Tue Oct 13 20:38:11 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 e38e1a7af019 -r 9a6e3bb0f358 hardcoded_params.json
--- a/hardcoded_params.json Wed Sep 23 14:59:36 2020 +0000
+++ b/hardcoded_params.json Tue Oct 13 20:38:11 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 e38e1a7af019 -r 9a6e3bb0f358 macros.xml
--- a/macros.xml Wed Sep 23 14:59:36 2020 +0000
+++ b/macros.xml Tue Oct 13 20:38:11 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>
       
       <requirement type="package" version="2.9.0">blast</requirement>
-      <requirement type="package" version="8.0.192">openjdk</requirement>

diff -r e38e1a7af019 -r 9a6e3bb0f358 macros_autotest.xml
--- a/macros_autotest.xml Wed Sep 23 14:59:36 2020 +0000
+++ b/macros_autotest.xml Tue Oct 13 20:38:11 2020 +0000

b'@@ -158,7 +158,6 @@\n <param name="compound_timeout" value="10"/>\n <param name="tree_timeout" value="0"/>\n <param name="top_n_hits" value="10"/>\n- <param name="cores" value="1"/>\n <param name="auto_charge" value="false"/>\n <param name="ion_tree" value="false"/>\n <param name="no_recalibration" value="false"/>\n@@ -228,7 +227,6 @@\n <param name="compound_timeout" value="10"/>\n <param name="tree_timeout" value="0"/>\n <param name="top_n_hits" value="10"/>\n- <param name="cores" value="1"/>\n <param name="auto_charge" value="false"/>\n <param name="ion_tree" value="false"/>\n <param name="no_recalibration" value="false"/>\n@@ -298,7 +296,6 @@\n <param name="compound_timeout" value="10"/>\n <param name="tree_timeout" value="0"/>\n <param name="top_n_hits" value="10"/>\n- <param name="cores" value="1"/>\n <param name="auto_charge" value="false"/>\n <param name="ion_tree" value="false"/>\n <param name="no_recalibration" value="false"/>\n@@ -368,7 +365,6 @@\n <param name="compound_timeout" value="10"/>\n <param name="tree_timeout" value="0"/>\n <param name="top_n_hits" value="10"/>\n- <param name="cores" value="1"/>\n <param name="auto_charge" value="false"/>\n <param name="ion_tree" value="false"/>\n <param name="no_recalibration" value="false"/>\n@@ -438,7 +434,6 @@\n <param name="compound_timeout" value="10"/>\n <param name="tree_timeout" value="0"/>\n <param name="top_n_hits" value="10"/>\n- <param name="cores" value="1"/>\n <param name="auto_charge" value="false"/>\n <param name="ion_tree" value="false"/>\n <param name="no_recalibration" value="false"/>\n@@ -508,7 +503,6 @@\n <param name="compound_timeout" value="100"/>\n <param name="tree_timeout" value="0"/>\n <param name="top_n_hits" value="10"/>\n- <param name="cores" value="1"/>\n <param name="auto_charge" value="false"/>\n <param name="ion_tree" value="false"/>\n <param name="no_recalibration" value="false"/>\n@@ -578,7 +572,6 @@\n <param name="compound_timeout" value="100"/>\n <param name="tree_timeout" value="0"/>\n <param name="top_n_hits" value="10"/>\n- <param name="cores" value="1"/>\n <param name="auto_charge" value="false"/>\n <param name="ion_tree" value="false"/>\n <param name="no_recalibration" value="false"/>\n@@ -648,7 +641,6 @@\n <param name="compound_timeout" value="100"/>\n <param name="tree_timeout" value="0"/>\n <param name="top_n_hits" value="10"/>\n- <param name="cores" value="1"/>\n <param name="auto_charge" value="false"/>\n <param name="ion_tree" value="false"/>\n <param name="no_recalibration" value="false"/>\n@@ -718,7 +710,6 @@\n <param name="compound_timeout" value="100"/>\n <param name="tree_timeout" value="0"/>\n <param name="top_n_hits" value="10"/>\n- <param name="cores" value="1"/>\n <param name="auto_charge" value="false"/>\n <param name="ion_tree" value="false"/>\n <param name="no_recalibration" value="false"/>\n@@ -760,9 +751,6 @@\n <test expect_num_outputs="3">\n <conditional name="adv_opts_cond">\n <param name="adv_opts_selector" value="advanced"/>\n- <param name="fragment_bin_tolerance" value="1.0005"/>\n- <param name="fragment_bin_offset" value="0.25"/>\n- <param name="instrument" value="high_res"/>\n <param name="use_A_ions" value="false"/>\n <param name="use_B_ions" value="true"/>\n <param name="use_C_ions" value="false"/>\n@@ -770,6 +758,7 @@\n <param name="use_Y_ions" value="true"/>\n <param name="use_Z_ions" value="false"/>\n <param name="use_NL_ions" value="false"/>\n+ <param name="second_enzyme" value=""/>\n <param name='..b' <param name="sort_by_size" value="false"/>\n </section>\n- <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>\n+ <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>\n <output name="ctd_out" ftype="xml">\n <assert_contents>\n <is_valid_xml/>\n@@ -25909,8 +26762,8 @@\n <param name="in" value="TOFCalibration_1_input.mzML"/>\n <output name="out" file="TOFCalibration_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>\n <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/>\n- <param name="ref_masses" value="TOFCalibration_ref_masses.txt" ftype="txt"/>\n- <param name="tof_const" value="TOFCalibration_const.csv" ftype="csv"/>\n+ <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>\n+ <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>\n <param name="peak_data" value="false"/>\n <section name="algorithm">\n <section name="PeakPicker">\n@@ -25991,8 +26844,8 @@\n <param name="in" value="TOFCalibration_2_input.mzML"/>\n <output name="out" file="TOFCalibration_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>\n <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/>\n- <param name="ref_masses" value="TOFCalibration_ref_masses.txt" ftype="txt"/>\n- <param name="tof_const" value="TOFCalibration_const.csv" ftype="csv"/>\n+ <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>\n+ <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>\n <param name="peak_data" value="true"/>\n <section name="algorithm">\n <section name="PeakPicker">\n@@ -26316,5 +27169,37 @@\n </assert_contents>\n </output>\n </test>\n- </xml>\n-<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>\n+ <test expect_num_outputs="2">\n+ <conditional name="adv_opts_cond">\n+ <param name="adv_opts_selector" value="advanced"/>\n+ <param name="force" value="false"/>\n+ <param name="test" value="true"/>\n+ </conditional>\n+ <param name="in" value="spectra.mzML"/>\n+ <output name="out" file="XTandemAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>\n+ <param name="database" value="proteinslong.fasta"/>\n+ <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/>\n+ <param name="ignore_adapter_param" value="false"/>\n+ <param name="precursor_mass_tolerance" value="5.0"/>\n+ <param name="fragment_mass_tolerance" value="0.3"/>\n+ <param name="precursor_error_units" value="ppm"/>\n+ <param name="fragment_error_units" value="Da"/>\n+ <param name="max_precursor_charge" value="0"/>\n+ <param name="no_isotope_error" value="false"/>\n+ <param name="fixed_modifications" value=""/>\n+ <param name="variable_modifications" value="Oxidation (M)"/>\n+ <param name="minimum_fragment_mz" value="150.0"/>\n+ <param name="enzyme" value="Trypsin"/>\n+ <param name="missed_cleavages" value="1"/>\n+ <param name="semi_cleavage" value="false"/>\n+ <param name="output_results" value="all"/>\n+ <param name="max_valid_expect" value="0.1"/>\n+ <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>\n+ <output name="ctd_out" ftype="xml">\n+ <assert_contents>\n+ <is_valid_xml/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </xml>\n+<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>\n'

diff -r e38e1a7af019 -r 9a6e3bb0f358 macros_test.xml
--- a/macros_test.xml Wed Sep 23 14:59:36 2020 +0000
+++ b/macros_test.xml Tue Oct 13 20:38:11 2020 +0000

b'@@ -177,20 +177,7 @@\n <output name="out" ftype="txt" value="MapStatistics2.txt"/>\n </test>\n </xml>\n-<xml name="manutest_MetaboliteAdductDecharger">\n- <test expect_num_outputs="3">\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="adv_opts_cond|test" value="true"/>\n- <param name="in" ftype="featurexml" value="Decharger_input.featureXML"/>\n- <output name="out_cm" ftype="consensusxml" value="MetaboliteAdductDecharger_cm.consensusXML" compare="sim_size"/>\n- <param name="OPTIONAL_OUTPUTS" value="out_fm_FLAG,outpairs_FLAG"/>\n- <output name="out_fm" ftype="featurexml" value="MetaboliteAdductDecharger_fm.featureXML" compare="sim_size"/>\n- <output name="outpairs" ftype="consensusxml" value="MetaboliteAdductDecharger_pairs.consensusXML" compare="sim_size"/>\n- </test>\n-</xml>\n <xml name="manutest_MetaboliteSpectralMatcher">\n- \n \n <test expect_num_outputs="1">\n <param name="adv_opts_selector" value="advanced"/>\n@@ -274,36 +261,46 @@\n </test>\n </xml>\n <xml name="manutest_OpenSwathDIAPreScoring">\n- \n \n-\n-\n-\n-\n-\n+ <test>\n+ <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>\n+ <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>\n+ <output_collection name="output_files" count="1">\n+ <element name="OpenSwathAnalyzer_2_swathfile_mzML.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>\n+ </output_collection>\n+ </test>\n+ \n+ \n+ <test>\n+ <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>\n+ <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/>\n+ <output_collection name="output_files" count="2">\n+ <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>\n+ <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>\n+ </output_collection>\n+ </test>\n </xml>\n \n <xml name="manutest_OpenSwathFileSplitter">\n-<test expect_num_outputs="3">\n- <conditional name="adv_opts_cond">\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="force" value="false"/>\n- <param name="test" value="true"/>\n- </conditional>\n- <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>\n- <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/>\n- <output_collection name="outputDirectory" count="6">\n- <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/>\n- <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/>\n- </output_collection>\n- <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>\n- <output name="ctd_out" ftype="xml">\n- <assert_contents>\n- <is_valid_xml/>\n- </assert_contents>\n- </output>\n-</test>\n+ <test expect_num_outputs="3">\n+ <conditional name="adv_opts_cond">\n+ <param name="adv_opts_selector" value="advanced"/>\n+ <param name="force" value="false"/>'..b'atureFinderMetabo"/><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>\n'

diff -r e38e1a7af019 -r 9a6e3bb0f358 prepare_test_data.sh
--- a/prepare_test_data.sh Wed Sep 23 14:59:36 2020 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1196 +0,0 @@\n-export COMET_BINARY="comet"\n-export CRUX_BINARY="crux"\n-export FIDOCHOOSEPARAMS_BINARY="FidoChooseParameters"\n-export FIDO_BINARY="Fido"\n-export LUCIPHOR_BINARY="$(dirname $(realpath $(which luciphor2)))/luciphor2.jar"\n-export MARACLUSTER_BINARY="/tmp/openms-stuff//OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster"\n-export MSFRAGGER_BINARY="/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar"\n-export MSGFPLUS_BINARY="$(msgf_plus -get_jar_path)"\n-export MYRIMATCH_BINARY="myrimatch"\n-export NOVOR_BINARY="/home/berntm/Downloads/novor/lib/novor.jar"\n-export OMSSA_BINARY="$(dirname $(realpath $(which omssacl)))/omssacl"\n-export PERCOLATOR_BINARY="percolator"\n-export SIRIUS_BINARY="$(which sirius)"\n-export SPECTRAST_BINARY="spectrast"\n-export XTANDEM_BINARY="xtandem"\n-export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"\n-FuzzyDiff -test -ini FuzzyDiff.ini -in1 FuzzyDiff_3_in1.featureXML -in2 FuzzyDiff_3_in2.featureXML > UTILS_FuzzyDiff_3.stdout 2> UTILS_FuzzyDiff_3.stderr\n-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$(cat UTILS_FuzzyDiff_3.stdout)";fi\n-IDMerger -test -in IDMerger_1_input1.idXML IDMerger_1_input2.idXML -out IDMerger_1_output.tmp -annotate_file_origin > TOPP_IDMerger_1.stdout 2> TOPP_IDMerger_1.stderr\n-if [[ "$?" -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\n-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\n-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$(cat TOPP_IDMerger_2.stdout)";fi\n-IDMerger -test -in IDMerger_1_input1.idXML IDMerger_1_input1.idXML -out IDMerger_3_output.tmp > TOPP_IDMerger_3.stdout 2> TOPP_IDMerger_3.stderr\n-if [[ "$?" -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\n-IDMerger -test -in degenerated_empty.idXML degenerated_empty.idXML -out IDMerger_4_output.tmp > TOPP_IDMerger_4.stdout 2> TOPP_IDMerger_4.stderr\n-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$(cat TOPP_IDMerger_4.stdout)";fi\n-IDMerger -test -in IDMerger_2_input1.idXML -add_to IDMerger_5_input1.idXML -out IDMerger_5_output.tmp > TOPP_IDMerger_5.stdout 2> TOPP_IDMerger_5.stderr\n-if [[ "$?" -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\n-BaselineFilter -test -in BaselineFilter_input.mzML -out BaselineFilter.tmp -struc_elem_length 1.5 > TOPP_BaselineFilter_1.stdout 2> TOPP_BaselineFilter_1.stderr\n-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$(cat TOPP_BaselineFilter_1.stdout)";fi\n-ConsensusMapNormalizer -test -in ConsensusMapNormalizer_input.consensusXML -out ConsensusMapNormalizer.tmp > TOPP_ConsensusMapNormalizer_1.stdout 2> TOPP_ConsensusMapNormalizer_1.stderr\n-if [[ "$?" -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\n-MapNormalizer -test -in MapNormalizer_input.mzML -out MapNormalizer.tmp > TOPP_MapNormalizer_1.stdout 2> TOPP_MapNormalizer_1.stderr\n-if [[ "$?" -ne "0" ]]; then >&2 echo \'TOPP_MapNormalizer_1 failed\'; >&2 echo -e "stderr:\\n$(cat TOPP_MapNormalizer_1.stderr | sed \'s/^/'..b'S_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\n-AssayGeneratorMetabo -test -executable "${SIRIUS_BINARY}" -in AssayGeneratorMetabo_input.mzML -in_id AssayGeneratorMetabo_ams_input.featureXML -out AssayGeneratorMetabo_ams_sirius_restrict_output.tmp.tsv -fragment_annotation sirius -use_exact_mass -transition_threshold 3.0 -min_transitions 2 -max_transitions 3 -min_fragment_mz 100 -max_fragment_mz 900 -preprocessing:filter_by_num_masstraces 1 -preprocessing:precursor_mz_tolerance 10 -preprocessing:precursor_mz_tolerance_unit ppm -preprocessing:feature_only -sirius:profile qtof -sirius:compound_timeout 100 > UTILS_AssayGeneratorMetabo_10.stdout 2> UTILS_AssayGeneratorMetabo_10.stderr\n-if [[ "$?" -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\n-SiriusAdapter -test -executable "${SIRIUS_BINARY}" -in SiriusAdapter_2_input.mzML -in_featureinfo SiriusAdapter_2_input.featureXML -out_sirius SiriusAdapter_4_output.tmp -out_fingerid SiriusAdapter_4_foutput.tmp -sirius:auto_charge -sirius:profile qtof -sirius:database all > TOPP_SiriusAdapter_4.stdout 2> TOPP_SiriusAdapter_4.stderr\n-if [[ "$?" -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\n-NovorAdapter -test -java_memory 512 -executable "${NOVOR_BINARY}" -in NovorAdapter_in.mzML -out NovorAdapter_1_out.tmp -variable_modifications "Acetyl (K)" -fixed_modifications "Carbamidomethyl (C)" -forbiddenResidues "I" > TOPP_NovorAdapter_1.stdout 2> TOPP_NovorAdapter_1.stderr\n-if [[ "$?" -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\n-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\n-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$(cat TOPP_SpectrastSearchAdapter_0_prepare.stdout)";fi\n-SpectraSTSearchAdapter -test -library_file testLib.splib -spectra_files SpectrastAdapter_1_hack.mzML -output_files SpectrastAdapter_1_out1.tmp.pep.xml -executable "${SPECTRAST_BINARY}" > TOPP_SpectrastSearchAdapter_1.stdout 2> TOPP_SpectrastSearchAdapter_1.stderr\n-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$(cat TOPP_SpectrastSearchAdapter_1.stdout)";fi\n-SpectraSTSearchAdapter -test -library_file testLib.splib -spectra_files SpectrastAdapter_1_hack.mzML -output_files SpectrastAdapter_1_out1.tmp.pep.tsv -executable "${SPECTRAST_BINARY}" > TOPP_SpectrastSearchAdapter_2.stdout 2> TOPP_SpectrastSearchAdapter_2.stderr\n-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$(cat TOPP_SpectrastSearchAdapter_2.stdout)";fi\n-LuciphorAdapter -test -in LuciphorAdapter_1_input.mzML -java_memory 1024 -id LuciphorAdapter_1_input.idXML -out LuciphorAdapter_1_output.tmp -executable "${LUCIPHOR_BINARY}" -min_num_psms_model 1 > TOPP_LuciphorAdapter_1.stdout 2> TOPP_LuciphorAdapter_1.stderr\n-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\n'

diff -r e38e1a7af019 -r 9a6e3bb0f358 prepare_test_data_manual.sh
--- a/prepare_test_data_manual.sh Wed Sep 23 14:59:36 2020 +0000
+++ b/prepare_test_data_manual.sh Tue Oct 13 20:38:11 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 e38e1a7af019 -r 9a6e3bb0f358 test-data.sh
--- a/test-data.sh Wed Sep 23 14:59:36 2020 +0000
+++ b/test-data.sh Tue Oct 13 20:38:11 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 e38e1a7af019 -r 9a6e3bb0f358 tools_blacklist.txt
--- a/tools_blacklist.txt Wed Sep 23 14:59:36 2020 +0000
+++ b/tools_blacklist.txt Tue Oct 13 20:38:11 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