Galaxy |

Changeset 11:7ca917175b23 (2020-10-13)

Previous changeset 10:4da16805dea6 (2020-09-24) Next changeset 12:0ced5bc9f4dd (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
OpenSwathAnalyzer.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 4da16805dea6 -r 7ca917175b23 404-urls.patch
--- a/404-urls.patch Thu Sep 24 12:33:57 2020 +0000
+++ b/404-urls.patch Tue Oct 13 19:43:44 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 4da16805dea6 -r 7ca917175b23 OpenSwathAnalyzer.xml
--- a/OpenSwathAnalyzer.xml Thu Sep 24 12:33:57 2020 +0000
+++ b/OpenSwathAnalyzer.xml Tue Oct 13 19:43:44 2020 +0000

[

@@ -98,6 +98,9 @@
         <expand macro="list_string_san"/>
       </param>
       <param name="im_extra_drift" argument="-algorithm:im_extra_drift" type="float" optional="true" min="0.0" value="0.0" label="Extra drift time to extract for IM scoring (as a fraction" help="e.g. 0.25 means 25% extra on each side)"/>
+      <param name="strict" argument="-algorithm:strict" type="text" optional="true" value="true" label="Whether to error (true) or skip (false) if a transition in a transition group does not have a corresponding chromatogram" help="">
+        <expand macro="list_string_san"/>
+      </param>
       <section name="TransitionGroupPicker" title="" help="" expanded="false">
         <param name="stop_after_feature" argument="-algorithm:TransitionGroupPicker:stop_after_feature" type="integer" optional="true" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
         <param name="stop_after_intensity_ratio" argument="-algorithm:TransitionGroupPicker:stop_after_intensity_ratio" type="float" optional="true" value="0.0001" label="Stop after reaching intensity ratio" help=""/>
@@ -207,12 +210,12 @@
       </section>
     </section>
     <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>
@@ -229,6 +232,6 @@
   <help><![CDATA[Picks peaks and finds features in an SWATH-MS or SRM experiment.

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

diff -r 4da16805dea6 -r 7ca917175b23 filetypes.txt
--- a/filetypes.txt Thu Sep 24 12:33:57 2020 +0000
+++ b/filetypes.txt Tue Oct 13 19:43:44 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 4da16805dea6 -r 7ca917175b23 generate-foo.sh
--- a/generate-foo.sh Thu Sep 24 12:33:57 2020 +0000
+++ b/generate-foo.sh Tue Oct 13 19:43:44 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 4da16805dea6 -r 7ca917175b23 generate.sh
--- a/generate.sh Thu Sep 24 12:33:57 2020 +0000
+++ b/generate.sh Tue Oct 13 19:43:44 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 4da16805dea6 -r 7ca917175b23 hardcoded_params.json
--- a/hardcoded_params.json Thu Sep 24 12:33:57 2020 +0000
+++ b/hardcoded_params.json Tue Oct 13 19:43:44 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 4da16805dea6 -r 7ca917175b23 macros.xml
--- a/macros.xml Thu Sep 24 12:33:57 2020 +0000
+++ b/macros.xml Tue Oct 13 19:43:44 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 4da16805dea6 -r 7ca917175b23 macros_autotest.xml
--- a/macros_autotest.xml Thu Sep 24 12:33:57 2020 +0000
+++ b/macros_autotest.xml Tue Oct 13 19:43:44 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 4da16805dea6 -r 7ca917175b23 macros_test.xml
--- a/macros_test.xml Thu Sep 24 12:33:57 2020 +0000
+++ b/macros_test.xml Tue Oct 13 19:43:44 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 4da16805dea6 -r 7ca917175b23 prepare_test_data.sh
--- a/prepare_test_data.sh Thu Sep 24 12:33:57 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 4da16805dea6 -r 7ca917175b23 prepare_test_data_manual.sh
--- a/prepare_test_data_manual.sh Thu Sep 24 12:33:57 2020 +0000
+++ b/prepare_test_data_manual.sh Tue Oct 13 19:43:44 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 4da16805dea6 -r 7ca917175b23 test-data.sh
--- a/test-data.sh Thu Sep 24 12:33:57 2020 +0000
+++ b/test-data.sh Tue Oct 13 19:43:44 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 4da16805dea6 -r 7ca917175b23 tools_blacklist.txt
--- a/tools_blacklist.txt Thu Sep 24 12:33:57 2020 +0000
+++ b/tools_blacklist.txt Tue Oct 13 19:43:44 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