# HG changeset patch # User galaxyp # Date 1607964861 0 # Node ID 59736982ab7b2001dada7580698d2cc7df70397a # Parent db2f5343536634513a89f3c72fc4af1e5ea254e3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms" diff -r db2f53435366 -r 59736982ab7b 404-urls.patch --- a/404-urls.patch Fri Nov 06 19:43:10 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -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 @@ - -+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.6.0/html/UTILS_FeatureFinderSuperHirn.html]]> - - diff -r db2f53435366 -r 59736982ab7b OMSSAAdapter.patch --- a/OMSSAAdapter.patch Fri Nov 06 19:43:10 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ ---- OMSSAAdapter.xml 2020-06-16 15:51:40.315400730 +0200 -+++ /tmp/OMSSAAdapter.xml 2020-06-16 15:50:23.536086074 +0200 -@@ -22,6 +22,7 @@ - mkdir database && - ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && - -+makeblastdb -dbtype prot -in 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && - ## Main program call - - set -o pipefail && diff -r db2f53435366 -r 59736982ab7b PSMFeatureExtractor.xml --- a/PSMFeatureExtractor.xml Fri Nov 06 19:43:10 2020 +0000 +++ b/PSMFeatureExtractor.xml Mon Dec 14 16:54:21 2020 +0000 @@ -1,7 +1,7 @@ - + Computes extra features for each input PSM. PSMFeatureExtractor @@ -17,7 +17,11 @@ ## Preprocessing mkdir in && +#if $in ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } +#else if $in_single + ln -s '$in_single' 'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' && +#end if mkdir out && ## Main program call @@ -27,7 +31,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && @EXECUTABLE@ -ini @EXECUTABLE@.ctd -in +#if $in ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} +#else if $in_single +'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' && +#end if -out 'out/output.${out_type}' @@ -41,7 +49,8 @@ - + + diff -r db2f53435366 -r 59736982ab7b PepNovoAdapter.patch --- a/PepNovoAdapter.patch Fri Nov 06 19:43:10 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ ---- PepNovoAdapter.xml 2020-05-12 15:55:24.712831518 +0200 -+++ /tmp/PepNovoAdapter.xml 2020-05-12 15:36:31.267276757 +0200 -@@ -42,8 +42,13 @@ - - - -- -- -+ -+ -+ -+ -+ -+ -+ - - - -@@ -51,8 +56,14 @@ - - - -- -- -+ -+ -+ -+ -+ -+ -+ -+ - - - diff -r db2f53435366 -r 59736982ab7b filetypes.txt --- a/filetypes.txt Fri Nov 06 19:43:10 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,85 +0,0 @@ -# CTD type # Galaxy type -# the following lines need to be at the top in order to ensure -# correct translation Galaxy->CTD type for the ambiguous cases -# (should only be relevant for the autogenerated tests [which -# do not set the ftype of the inputs]) -txt txt -tsv tabular - -##analysisXML -# XTandemAdapter output is named xml in OMS (which is to unspecific) and bioml in Galaxy .. so this is renamed via hardcoded parameters -bioml xml -consensusXML consensusxml -# TODO csv is problematic, since csv often actually means tsv .. but not always -csv csv -##dat -dta dta -dta2d dta2d -edta edta -fa fasta -fas fasta -fasta fasta -FASTA fasta -featureXML featurexml -featurexml featurexml -# fid -html html -HTML html -idXML idxml -##ini txt -json json -kroenik kroenik -mascotXML mascotxml -mgf mgf -mrm mrm -ms sirius.ms -ms2 ms2 -msp msp -mzData mzdata -mzid mzid -# important to have mzML first, since LuciphorAdapter is case sensitive https://github.com/OpenMS/OpenMS/issues/4444 -mzML mzml -mzml mzml -mzq mzq -mzTab mztab -mzXML mzxml -novor txt -obo obo -# I guess this is the idXML output of omssa -omssaXML idxml -osw osw -OSW osw -params txt -paramXML paramxml -fasta peff -peplist peplist -# TODO pep.xml should be removed with OMS 2.6 https://github.com/OpenMS/OpenMS/pull/4541 .. but still in the tests -pep.xml pepxml -pepXML pepxml -png png -PNG png -protXML protxml -psms psms -# TODO implement or use -# psq -pqp pqp -qcML qcml -spec.xml spec.xml -splib splib -sqMass sqmass -tandem.xml tandem -trafoXML trafoxml -traML traml -TraML traml -tab tabular -## MOVED TO TOP txt txt -raw thermo.raw -## xls: SpectraSTSearchAdapter https://github.com/OpenMS/OpenMS/pull/4419 -xls tsv -XML xml -xml xml -xquest.xml xquest.xml -xsd xml - -# TODO needs to be implemented, needs to be below xml in order that Galaxy->OMS mapping gives xml -# cachedMzML xml diff -r db2f53435366 -r 59736982ab7b fill_ctd_clargs.py --- a/fill_ctd_clargs.py Fri Nov 06 19:43:10 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +0,0 @@ -#!/usr/bin/env python3 -from argparse import ArgumentParser -from io import StringIO - -from CTDopts.CTDopts import ( - CTDModel, - ModelTypeError, - Parameters -) - -if __name__ == "__main__": - # note add_help=False since otherwise arguments starting with -h will - # trigger an error (despite allow_abbreviate) - parser = ArgumentParser(prog="fill_ctd_clargs", - description="fill command line arguments" - "into a CTD file and write the CTD file to", - add_help=False, allow_abbrev=False) - parser.add_argument("--ctd", dest="ctd", help="input ctd file", - metavar='CTD', default=None, required=True) - args, cliargs = parser.parse_known_args() - # load CTDModel - model = None - try: - model = CTDModel(from_file=args.ctd) - except ModelTypeError: - pass - try: - model = Parameters(from_file=args.ctd) - except ModelTypeError: - pass - assert model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ctd) - - # get a dictionary of the ctd arguments where the values of the parameters - # given on the command line are overwritten - margs = model.parse_cl_args(cl_args=cliargs, ignore_required=True) - - # write the ctd with the values taken from the dictionary - out = StringIO() - ctd_tree = model.write_ctd(out, margs) - print(out.getvalue()) diff -r db2f53435366 -r 59736982ab7b generate.sh --- a/generate.sh Fri Nov 06 19:43:10 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,76 +0,0 @@ -#!/usr/bin/env bash - -VERSION=2.6 -FILETYPES="filetypes.txt" -PROFILE="20.05" -## FILETYPES_RE=$(grep -v "^#" $FILETYPES | grep -v "^$" | cut -f 1 -d" " | tr '\n' '|' | sed 's/|$//'| sed 's/|/\\|/g') - -export tmp=$(mktemp -d) -export CTDCONVERTER="$tmp/CTDConverter" - -############################################################################### -## reset old data -############################################################################### -# rm $(ls *xml |grep -v macros) -# rm -rf ctd -# mkdir -p ctd -# echo "" > prepare_test_data.sh - -############################################################################### -## generate tests -## also creates -## - conda environment (for executing the binaries) and -## - the git clone of OpenMS (for generating the tests) -## - ctd files -############################################################################### -bash ./test-data.sh ./macros_autotest.xml - -############################################################################### -## get the -## - conda package (for easy access and listing of the OpenMS binaries), -############################################################################### -# if [ ! -d $OPENMSPKG ]; then -# mkdir $OPENMSPKG/ -# wget -P $OPENMSPKG/ "$CONDAPKG" -# tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C OpenMS$VERSION-pkg/ -# rm $OPENMSPKG/"$(basename $CONDAPKG)" -# fi - -############################################################################### -## Get python libaries for CTD -> Galaxy conversion -## TODO fix to main repo OR conda packkage if PRs are merged -############################################################################### -# if [ ! -d CTDopts ]; then -# # git clone https://github.com/genericworkflownodes/CTDopts CTDopts -# git clone -b topic/no-1-2x https://github.com/bernt-matthias/CTDopts CTDopts -# fi -if [ ! -d $CTDCONVERTER ]; then - #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter - git clone -b topic/cdata https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER -fi -# export PYTHONPATH=$(pwd)/CTDopts -############################################################################### -## conversion ctd->xml -############################################################################### - -find . -maxdepth 0 -name "[A-Z]*xml" -delete -source $(dirname $(which conda))/../etc/profile.d/conda.sh -conda activate $tmp/OpenMS$VERSION-env -python $CTDCONVERTER/convert.py galaxy -i ctd/*ctd -o ./ -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p hardcoded_params.json --test-macros macros_autotest.xml --test-macros-prefix autotest_ --test-macros macros_test.xml --test-macros-prefix manutest_ --tool-version $VERSION --tool-profile $PROFILE > convert.out 2> convert.err -if [[ "$?" -ne "0" ]]; then >&2 echo 'CTD -> XML conversion failed'; >&2 echo -e "stderr:\n$(cat convert.err)"; fi -conda deactivate - -patch PepNovoAdapter.xml < PepNovoAdapter.patch -patch OMSSAAdapter.xml < OMSSAAdapter.patch - -# https://github.com/OpenMS/OpenMS/pull/4984 -sed -i -e 's@http://www.openms.de/documentation/@http://www.openms.de/doxygen/release/2.6.0/html/@' ./*xml -# https://github.com/OpenMS/OpenMS/pull/4984#issuecomment-702641976 -patch -p0 <404-urls.patch - -# #-b version log debug test in_type executable pepnovo_executable param_model_directory rt_concat_trafo_out param_id_pool - -# for i in A-E F-H I-L M-N O-P Q-Z -# do -# planemo t [$i]*xml --galaxy_branch release_20.05 --galaxy_python_version 3.7 --test_output $i.html --test_output_json $i.json & -# done diff -r db2f53435366 -r 59736982ab7b hardcoded_params.json --- a/hardcoded_params.json Fri Nov 06 19:43:10 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,236 +0,0 @@ -{ - "#": "blacklist parameters", - - "version": [{"value": "@"}], - "debug": [{"value": "@"}], - "algorithm:debug": [{"value": "@"}], - "java_memory": [{"value": "@"}], - "java_permgen": [{"value": "@"}], - "#": "type of input is always determined from the file extension ", - "in_type": [{"value": "@"}], - - "#": "tool specific blacklist parameters", - - "convert_back": [{"value": "@", "tools": ["OpenSwathMzMLFileCacher"]}], - "NET_executable": [{ - "value": "@", - "tools": ["FileConverter"] - }], - - - "params_file": [{"value": "@", "tools": ["SpectraSTSearchAdapter"]}], - - "#": "TODO not usable in 2.5 https://github.com/OpenMS/OpenMS/issues/4456, corresponding test currently disabled", - "consensus_out": [{"value": "@", "tools": ["MaRaClusterAdapter"]}], - "#": "TODO would need treatment as prefix-output", - "output_directory": [{"value": "@", "tools": ["MaRaClusterAdapter"]}], - - "#": "hardcode parameter values", - - "comet_version": [{ - "value":"2016.01 rev. 3" - }], - "comet_executable": [{ - "value":"comet" - }], - "crux_executable": [{ - "value": "crux" - }], - "fido_executable": [{ - "value":"Fido" - }], - "fidocp_executable": [{ - "value":"FidoChooseParameters" - }], - "maracluster_executable": [{ - "value":"/home/berntm/projects/tools-galaxyp/tools/openms/OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster" - }], - "mascot_directory": [{ - "value":"TODO" - }], - "myrimatch_executable": [{ - "value":"myrimatch" - }], - "omssa_executable": [{ - "value":"$(dirname $(realpath $(which omssacl)))/omssacl" - }], - "ThermoRaw_executable": [{ - "value": "ThermoRawFileParser.exe", - "tools": ["FileConverter"] - }], - "pepnovo_executable": [{ - "value":"pepnovo" - }], - "percolator_executable": [{ - "value":"percolator" - }], - "xtandem_executable": [{ - "value":"xtandem" - }], - "executable": [ - { - "value":"$(dirname $(realpath $(which luciphor2)))/luciphor2.jar", - "tools": ["LuciphorAdapter"] - }, { - "value":"/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar", - "tools": ["MSFraggerAdapter"] - }, { - "value":"$(msgf_plus -get_jar_path)", - "tools": ["MSGFPlusAdapter"] - }, { - "value": "/home/berntm/Downloads/novor/lib/novor.jar", - "tools": ["NovorAdapter"] - }, { - "value":"$(which sirius)", - "tools": ["SiriusAdapter", "AssayGeneratorMetabo"] - }, { - "value":"spectrast", - "tools": ["SpectraSTSearchAdapter"] - } - ], - "r_executable": [{ - "value":"R" - }], - "rscript_executable": [{ - "value":"Rscript" - }], - "java_executable": [{ - "value":"java" - }], - "log": [{ - "value":"log.txt" - }], - "tempDirectory": [{ - "value":"$TMP_DIR" - }], - "temp_data_directory": [{ - "value":"$TMP_DIR" - }], - "algorithm:Preprocessing:tmp_dir": [{ - "value":"$TMP_DIR" - }], - "no_progress": [{ - "value": true - }], - "#": "only used in LuciphorAdapter at the moment, inconsistency will be fixed", - "num_threads": [{ - "value":"${GALAXY_SLOTS:-1}" - }], - "threads": [{ - "value": "${GALAXY_SLOTS:-1}" - }], - "sirius:cores": [{ - "value": "${GALAXY_SLOTS:-1}" - }], - - "#": "hardcode the outer loop threads for OpenSwathWorkflow", - "outer_loop_threads": [{ - "value": "1", - "tools": ["OpenSwathWorkflow"] - }], - "separator": [{ - "value": ",", - "tools": ["IDMassAccuracy"] - }], - - "#": "don't alow to copy data internally to save computation time for reloading", - "copy_data": [{ - "value": "false", - "tools": ["MapAlignerTreeGuided"] - }], - - "#": "overwrite/add Galaxy xml attributes of some parameters (names need to start with param_)", - - "#": "test is not a hardcoded value since we need to set it in the tool tests", - "test": [{ - "CTD:type": "text", - "XML:type": "hidden" - }], - - "#": "overwrite CTD attributes of some parameters (some are not possible, e.g. type)", - - "#": "for some tools the user needs to select the desired output type since detection by extension makes no sense for galaxy tools", - "out_type": [{ - "CTD:required": true, - "CTD:advanced": false - }], - - "#": "SeedListGenerator with consensusXML input needs a dynamic number of outputs that depends on the content of the input, so we remove this options at the moment because its hard or impossible to implement in Galaxy, https://github.com/OpenMS/OpenMS/issues/4404 .. see also in parameter", - "#": "FileInfo, MapStatistics, SequenceCoverageCalculator wo -out just writes to stdout. not wanted here", - "#": "MzMLSplitter output prefix https://github.com/OpenMS/OpenMS/issues/4404", - "#": "IDRipper: blacklist out (is doing the same as the output-prefix out-path)", - "out": [{ - "CTD:is_list": false, - "tools": ["SeedListGenerator"] - }, { - "CTD:required": true, - "tools": ["FileInfo", "MapStatistics", "SequenceCoverageCalculator"] - }, { - "CTD:type": "output-prefix", - "CTD:required": true, - "CTD:restrictions": "mzml", - "tools": ["MzMLSplitter"] - }, { - "value": "@", - "tools": ["IDRipper"] - }], - - "#": "Try to remove xml data type whereever possible", - "#": "XTandem Adapter output is called .xml in OMS which is to unspecific -> use Galaxy's bioml", - "xml_out": [{ - "CTD:restrictions": "bioml", - "tools": ["XTandemAdapter"] - }], - - "#": "IDFileConverter remove xml", - "#": "OpenSwathWorkflow make in single file input and all outputs non-optional", - "#": "XFDR does not need xml .. redundant with xquest.xml TODO check if list is up to date with each new release", - "#": "SeedListGenerator: remove consensusXML https://github.com/OpenMS/OpenMS/issues/4404 .. see also out parameter", - "in": [{ - "CTD:restrictions": "pepXML,protXML,mascotXML,omssaXML,bioml,psms,tsv,idXML,mzid,xquest.xml", - "tools": ["IDFileConverter"] - }, { - "CTD:is_list": false, - "tools": ["OpenSwathWorkflow"] - }, { - "CTD:restrictions": "idXML,mzid,xquest.xml", - "tools": ["XFDR"] - }, { - "CTD:restrictions": "mzML,idXML,featureXML", - "tools": ["SeedListGenerator"] - }], - - "#": "IDMapper has in and spectra:in params, in is used in out as format_source", - "#": "which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493", - "spectra:in": [{ - "CTD:name": "_in", - "tools": ["IDMapper"] - }], - - "#": "hardcoding prefix parameters which are not yet available in OMS but in CTDOpts https://github.com/OpenMS/OpenMS/pull/4527", - "#": "output-prefix", - "out_path": [{ - "CTD:type": "output-prefix", - "CTD:required": true, - "CTD:restrictions": "idXML", - "tools": ["IDRipper"] - }], - "outputDirectory": [{ - "CTD:type": "output-prefix", - "CTD:advanced": false, - "CTD:required": true, - "CTD:restrictions": "mzml", - "tools": ["OpenSwathFileSplitter"] - }], - - "#": "OpenSwathDIAPreScoring: https://github.com/OpenMS/OpenMS/pull/4443", - "#": "SpectraSTSearchAdapter does not need xml .. redundant with pep.xml TODO check if list is up to date with each new release", - "output_files": [{ - "CTD:required": true, - "tools": ["OpenSwathDIAPreScoring"] - }, { - "CTD:restrictions": "txt,tsv,pep.xml,pepXML,html", - "tools": ["SpectraSTSearchAdapter"] - - }] -} diff -r db2f53435366 -r 59736982ab7b macros.xml --- a/macros.xml Fri Nov 06 19:43:10 2020 +0000 +++ b/macros.xml Mon Dec 14 16:54:21 2020 +0000 @@ -21,6 +21,7 @@ + diff -r db2f53435366 -r 59736982ab7b macros_autotest.xml --- a/macros_autotest.xml Fri Nov 06 19:43:10 2020 +0000 +++ b/macros_autotest.xml Mon Dec 14 16:54:21 2020 +0000 @@ -126,7 +126,6 @@ -
@@ -195,7 +194,6 @@ -
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r db2f53435366 -r 59736982ab7b macros_test.xml --- a/macros_test.xml Fri Nov 06 19:43:10 2020 +0000 +++ b/macros_test.xml Mon Dec 14 16:54:21 2020 +0000 @@ -335,6 +335,7 @@ + @@ -354,6 +355,13 @@ + + + + + + + diff -r db2f53435366 -r 59736982ab7b prepare_test_data_manual.sh --- a/prepare_test_data_manual.sh Fri Nov 06 19:43:10 2020 +0000 +++ b/prepare_test_data_manual.sh Mon Dec 14 16:54:21 2020 +0000 @@ -86,10 +86,13 @@ PhosphoScoring -in spectra.mzML -id MSGFPlusAdapter_1_out1.tmp -out PhosphoScoring.idxml > PhosphoScoring.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out PSMFeatureExtractor.idxml > PSMFeatureExtractor_1.stdout 2> stderr +# TODO PSMFeatureExtractor should have auto tests with 2.7 https://github.com/OpenMS/OpenMS/pull/5087 +PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out_type idXML -out PSMFeatureExtractor.idxml > PSMFeatureExtractor_1.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out PSMFeatureExtractor.mzid > PSMFeatureExtractor_2.stdout 2> stderr +PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out_type mzid -out PSMFeatureExtractor.mzid > PSMFeatureExtractor_2.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi +PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML -out_type idXML -out PSMFeatureExtractor_3.idXML > PSMFeatureExtractor_3.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_3 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi QCCalculator -test -in OpenPepXL_input.mzML -out QCCalculator1.qcML > QCCalculator_1.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'QCCalculator_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi diff -r db2f53435366 -r 59736982ab7b readme.md --- a/readme.md Fri Nov 06 19:43:10 2020 +0000 +++ b/readme.md Mon Dec 14 16:54:21 2020 +0000 @@ -22,11 +22,14 @@ Manual updates should only be done to -- the `@GALAXY_VERSION@"` token in `macros.xml` - and the manually contributed tests in `macros_test.xml` (The goal is that all tools that do not have an automatically generated test are covered here) - the `hardcoded_params.json` files +Wrapper versions are managed in `bump.json`. For tools listed in the file +the wrapper version will be set accordingly and otherwise `0` is used. +For a major update of the tool version the bump file should be reset (to `{}`). + In a few cases patches may be acceptable. Installation diff -r db2f53435366 -r 59736982ab7b test-data/pepnovo_models.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pepnovo_models.loc Mon Dec 14 16:54:21 2020 +0000 @@ -0,0 +1,13 @@ +#name value path +default_models CID_IT_TRYP ${__HERE__}/pepnovo_models/ +default_models LTQ_COMP ${__HERE__}/pepnovo_models/ +default_models DBC4_PEAK ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_TAG5 ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_TAG6 ${__HERE__}/pepnovo_models/ +default_models ITDNV_PEAK ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_SCORE ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_TAG3 ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_DNVPART ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_TAG4 ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_DB ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_CSP ${__HERE__}/pepnovo_models/ diff -r db2f53435366 -r 59736982ab7b test-data/random.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random.fa Mon Dec 14 16:54:21 2020 +0000 @@ -0,0 +1,18 @@ +>RND24402 Randomly generated sequence, created by ExPASy tool RandSeq, using average amino acid composition +LALLTDKYSVTKSIKGYAGQQQKCTDDEGLAEDSAAMSLVPIRAAWTISVSVDLFYLGIV +TNVTKDSVEHLVGIPLVTHEFMASRCEMRGQVVSATFGSWQKAESKAYRIPLKATPLDEF +VESAVYLFGGSSNEYECVLIGNSHPVLIFLDIDAVPGARKPRTGFFMAEGFHSKGETRAL +VGKSPPLGEYRKGAFHFTFPIKEAIRLGPPKKRIMGYRDALEGGLNHYVQTQVLVLLPMI +QVARRWENGLGLLVGKFLKLPTHPLDLNQVTLCWSEAVTEDNKRFLLTIKTSAQGKSAPT +SHINYVPQHNSMELMAINGSPFAAQHKSNDEIESMRDLSKLYADAETLESHGERGVRHQA +TETKISKVTNLRRKLPQLLDLNVVDNACNWESVGAHVLEYVLVNLYLKELQEPKVELQPR +LNETTMKAGASSLGVESGASAHSFYKGGVSEAKLRFRHVATPAAARIWWCVVMFRINRRY +DGITYNSVGEQLSGVHEYVRAAQLFGLTTGKNLRSTGIVIIKLSTAIDLECLVQAKPKEA +YVLANDYIGAKPHPARLETGPALVLFIVETINNDTLNAAILITALGGKFLNVRPDLLFGV +QALFGCVRMFRHADCTIGREKFVQTEISHKAKFLYEINEFFLERILQFEEAKSPVGAPAY +DIPIGRGLVMDSSTDLWNIYVVELISGQEKRTGIDPDTPMGTSHNLYMTDARLDERDQRS +FLNSEFVKPSKLANGSEWADPYVEPDKTEVIAFFPATLIVIMADGSALNGQVCIQPAKDN +SKMADDLATVHIGQDRPCDWGISASHEYDEVNRPARINGVMMQQLMAEDNQGPGASPRDQ +MGDADDLKEIKWNKYVIDNEIIGRERGISAERVKIFLGDTLTARGLLDSPPGQTKVFDLR +PRQSDKNQSGMFKRDQNAMYFPLEYDRIGAQTDTGSLYSTLITKFASISIDLVKLSMPRE +KQIDEERLHSEFIENQKRSALPAVQKNLACISCVEACRGT diff -r db2f53435366 -r 59736982ab7b test-data/random_RNA.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_RNA.fa Mon Dec 14 16:54:21 2020 +0000 @@ -0,0 +1,2 @@ +> random RNA +GUGUUACUGCCACGAAACAAAAUGUUCAAGACACCGGGCGCCAUCUGUAUAUUACUCGCCAAUCAGACGGUCUGCAACGCUACAGACAUGGAGCUCAGCGCUGACGAUGUCGCCGGACCAAGUACGAUCACUUUGCUCGUGCAAAUGUUCGUCCGCAUUGGGCACUAUAACUCGAAUUGUCGAAUCCGGGUGGCGAGCCGCCACUUAUAGGAUAAAUAUUCAAACUAACAUUAUGGCGCCAAAUCUGCAAUCUCUACUUUAGACAUUAUAUACCCACAUUUACAAUUAGAGUUAUUAUUAGUUAACGUGUGCCAGAGCAGGGAUGGCUCUUGUCAGCCAUAGUUGUGUGAACGGGCUGUAUUUCCUUCCUAAUUAUAGAGCGGCACCGGAAAGCAAUGCACGAUCCACGAGGGCACUUCACAUGGUCACAAACAGUCAUUCUGGUACCCUGAUUCGUUCCCGAAAGGGAAGUAUAUACACGGCCCCCGUGUAUAUCGCCAGUCACACGGCAGGAGCGAGAGUUCGUUUGUAUACAUGCCCAGGAGCCUUCUCUAACUUUUGAAGCUGUGCAACUUUGUUGGCGCGUCACCACUAAGUCAGCUUAAUAGACAGCAGAUGGGAGAAUUUACCAUUUCAUUUUGUCCGAGCUGAUACCGGUAGGUCAUCUCUAAUCACCCGUUAUCCUCUCGUAAUAUAAUCGCUACUAAGGUAUGAAGGUGUCUGCGAAAGGUAACGUAAAUCAUUCUCGGCUCCUUGCAAAGUACGACUAGGAUCCAUCGUACACAUCCGGACGAAGAUGUAAAAUUGACGCCCCUGUAGGCCGUGAGACAGACGUGAGCCAAACCAUCUGCUCUACUUCUGGAGGCCUUGAAUAGUGGCGCGUUGUGUAAUCUUAAGAGAGAUUUUACUUGGAAUUACAGCCUACUUUGACCAGUAGCGCAUUGUGAACAAAUAUUCCCGUACGCGUCCAAUUGCAGCAAAACGUGGGCCUGUGUCCAGU diff -r db2f53435366 -r 59736982ab7b test-data/spectrast.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/spectrast.log Mon Dec 14 16:54:21 2020 +0000 @@ -0,0 +1,22 @@ +START: (Sun Dec 13 17:22:43 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEpepXML -sO/tmp SpectrastAdapter_1_hack.mzML +GENERAL: File offset size is 8 bytes. Big library supported. +GENERAL: Pointer size is 8 bytes. +MZXML SEARCH: Sorted query spectra in "SpectrastAdapter_1_hack.mzML" by precursor m/z +MZXML SEARCH: Searched "SpectrastAdapter_1_hack.mzML" (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1) +MZXML SEARCH: Searched 1 files total (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1) +SEARCH STATS: Breakdown: +1 = 0 ; +2 = 0 ; +3 = 0 ; +4 = 0 ; +5 = 0 ; +PERFORMANCE: Total Run Time = 0 seconds. Total Number of Searches Performed = 3. Run Time per Search = 0 seconds.. + +END: (Sun Dec 13 17:22:43 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEpepXML -sO/tmp SpectrastAdapter_1_hack.mzML +========== +START: (Sun Dec 13 17:22:43 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEtsv -sO/tmp SpectrastAdapter_1_hack.mzML +GENERAL: File offset size is 8 bytes. Big library supported. +GENERAL: Pointer size is 8 bytes. +MZXML SEARCH: Sorted query spectra in "SpectrastAdapter_1_hack.mzML" by precursor m/z +MZXML SEARCH: Searched "SpectrastAdapter_1_hack.mzML" (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1) +MZXML SEARCH: Searched 1 files total (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1) +SEARCH STATS: Breakdown: +1 = 0 ; +2 = 0 ; +3 = 0 ; +4 = 0 ; +5 = 0 ; +PERFORMANCE: Total Run Time = 1 seconds. Total Number of Searches Performed = 3. Run Time per Search = 0.333333 seconds.. + +END: (Sun Dec 13 17:22:44 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEtsv -sO/tmp SpectrastAdapter_1_hack.mzML +========== diff -r db2f53435366 -r 59736982ab7b tools_blacklist.txt --- a/tools_blacklist.txt Fri Nov 06 19:43:10 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -# seems not possible for 2.5 https://github.com/OpenMS/OpenMS/issues/4426 -# DigestorMotif - -# deprecated https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/UTILS_IDDecoyProbability.html -# https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/a16242.html -IDDecoyProbability - -# personal communication with author V. Bafna: -# "InsPect is no longer maintained as there are many better tools including MS-GF+" -InspectAdapter - -# licence? see https://github.com/bioconda/bioconda-recipes/issues/18953 -#MSFraggerAdapter - -# https://github.com/OpenMS/OpenMS/issues/4550#issuecomment-594065727 -ProteomicsLFQ - -# https://github.com/OpenMS/OpenMS/issues/4401 -InclusionExclusionListCreator -RTPredict -PTPredict