# HG changeset patch
# User galaxyp
# Date 1607964899 0
# Node ID cab9b21eabf95222e66bed547be8c099eec714d1
# Parent bd5d779a7a3817719362a0bbe4ca3da6dd0f4560
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms"
diff -r bd5d779a7a38 -r cab9b21eabf9 404-urls.patch
--- a/404-urls.patch Fri Nov 06 20:37:11 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 bd5d779a7a38 -r cab9b21eabf9 LuciphorAdapter.xml
--- a/LuciphorAdapter.xml Fri Nov 06 20:37:11 2020 +0000
+++ b/LuciphorAdapter.xml Mon Dec 14 16:54:59 2020 +0000
@@ -1,7 +1,7 @@
-
+
Modification site localisation using LuciPHOr2.
LuciphorAdapter
diff -r bd5d779a7a38 -r cab9b21eabf9 OMSSAAdapter.patch
--- a/OMSSAAdapter.patch Fri Nov 06 20:37:11 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 bd5d779a7a38 -r cab9b21eabf9 PepNovoAdapter.patch
--- a/PepNovoAdapter.patch Fri Nov 06 20:37:11 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 @@
-
-
-
--
--
-+
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-@@ -51,8 +56,14 @@
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diff -r bd5d779a7a38 -r cab9b21eabf9 filetypes.txt
--- a/filetypes.txt Fri Nov 06 20:37:11 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 bd5d779a7a38 -r cab9b21eabf9 fill_ctd_clargs.py
--- a/fill_ctd_clargs.py Fri Nov 06 20:37:11 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 bd5d779a7a38 -r cab9b21eabf9 generate.sh
--- a/generate.sh Fri Nov 06 20:37:11 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 $i.json &
-# done
diff -r bd5d779a7a38 -r cab9b21eabf9 hardcoded_params.json
--- a/hardcoded_params.json Fri Nov 06 20:37:11 2020 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,236 +0,0 @@
-{
- "#": "blacklist parameters",
-
- "version": [{"value": "@"}],
- "debug": [{"value": "@"}],
- "algorithm:debug": [{"value": "@"}],
- "java_memory": [{"value": "@"}],
- "java_permgen": [{"value": "@"}],
- "#": "type of input is always determined from the file extension ",
- "in_type": [{"value": "@"}],
-
- "#": "tool specific blacklist parameters",
-
- "convert_back": [{"value": "@", "tools": ["OpenSwathMzMLFileCacher"]}],
- "NET_executable": [{
- "value": "@",
- "tools": ["FileConverter"]
- }],
-
-
- "params_file": [{"value": "@", "tools": ["SpectraSTSearchAdapter"]}],
-
- "#": "TODO not usable in 2.5 https://github.com/OpenMS/OpenMS/issues/4456, corresponding test currently disabled",
- "consensus_out": [{"value": "@", "tools": ["MaRaClusterAdapter"]}],
- "#": "TODO would need treatment as prefix-output",
- "output_directory": [{"value": "@", "tools": ["MaRaClusterAdapter"]}],
-
- "#": "hardcode parameter values",
-
- "comet_version": [{
- "value":"2016.01 rev. 3"
- }],
- "comet_executable": [{
- "value":"comet"
- }],
- "crux_executable": [{
- "value": "crux"
- }],
- "fido_executable": [{
- "value":"Fido"
- }],
- "fidocp_executable": [{
- "value":"FidoChooseParameters"
- }],
- "maracluster_executable": [{
- "value":"/home/berntm/projects/tools-galaxyp/tools/openms/OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster"
- }],
- "mascot_directory": [{
- "value":"TODO"
- }],
- "myrimatch_executable": [{
- "value":"myrimatch"
- }],
- "omssa_executable": [{
- "value":"$(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 bd5d779a7a38 -r cab9b21eabf9 macros.xml
--- a/macros.xml Fri Nov 06 20:37:11 2020 +0000
+++ b/macros.xml Mon Dec 14 16:54:59 2020 +0000
@@ -21,6 +21,7 @@
+
diff -r bd5d779a7a38 -r cab9b21eabf9 macros_autotest.xml
--- a/macros_autotest.xml Fri Nov 06 20:37:11 2020 +0000
+++ b/macros_autotest.xml Mon Dec 14 16:54:59 2020 +0000
@@ -126,7 +126,6 @@
-
@@ -195,7 +194,6 @@
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-
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-
@@ -25731,7 +25716,6 @@
-
-
+
diff -r bd5d779a7a38 -r cab9b21eabf9 macros_discarded_auto.xml
--- a/macros_discarded_auto.xml Fri Nov 06 20:37:11 2020 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,378 +0,0 @@
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diff -r bd5d779a7a38 -r cab9b21eabf9 macros_test.xml
--- a/macros_test.xml Fri Nov 06 20:37:11 2020 +0000
+++ b/macros_test.xml Mon Dec 14 16:54:59 2020 +0000
@@ -335,6 +335,7 @@
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@@ -354,6 +355,13 @@
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diff -r bd5d779a7a38 -r cab9b21eabf9 prepare_test_data_manual.sh
--- a/prepare_test_data_manual.sh Fri Nov 06 20:37:11 2020 +0000
+++ b/prepare_test_data_manual.sh Mon Dec 14 16:54:59 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 bd5d779a7a38 -r cab9b21eabf9 readme.md
--- a/readme.md Fri Nov 06 20:37:11 2020 +0000
+++ b/readme.md Mon Dec 14 16:54:59 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 bd5d779a7a38 -r cab9b21eabf9 test-data/pepnovo_models.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pepnovo_models.loc Mon Dec 14 16:54:59 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 bd5d779a7a38 -r cab9b21eabf9 test-data/random.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/random.fa Mon Dec 14 16:54:59 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 bd5d779a7a38 -r cab9b21eabf9 test-data/random_RNA.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/random_RNA.fa Mon Dec 14 16:54:59 2020 +0000
@@ -0,0 +1,2 @@
+> random RNA
+GUGUUACUGCCACGAAACAAAAUGUUCAAGACACCGGGCGCCAUCUGUAUAUUACUCGCCAAUCAGACGGUCUGCAACGCUACAGACAUGGAGCUCAGCGCUGACGAUGUCGCCGGACCAAGUACGAUCACUUUGCUCGUGCAAAUGUUCGUCCGCAUUGGGCACUAUAACUCGAAUUGUCGAAUCCGGGUGGCGAGCCGCCACUUAUAGGAUAAAUAUUCAAACUAACAUUAUGGCGCCAAAUCUGCAAUCUCUACUUUAGACAUUAUAUACCCACAUUUACAAUUAGAGUUAUUAUUAGUUAACGUGUGCCAGAGCAGGGAUGGCUCUUGUCAGCCAUAGUUGUGUGAACGGGCUGUAUUUCCUUCCUAAUUAUAGAGCGGCACCGGAAAGCAAUGCACGAUCCACGAGGGCACUUCACAUGGUCACAAACAGUCAUUCUGGUACCCUGAUUCGUUCCCGAAAGGGAAGUAUAUACACGGCCCCCGUGUAUAUCGCCAGUCACACGGCAGGAGCGAGAGUUCGUUUGUAUACAUGCCCAGGAGCCUUCUCUAACUUUUGAAGCUGUGCAACUUUGUUGGCGCGUCACCACUAAGUCAGCUUAAUAGACAGCAGAUGGGAGAAUUUACCAUUUCAUUUUGUCCGAGCUGAUACCGGUAGGUCAUCUCUAAUCACCCGUUAUCCUCUCGUAAUAUAAUCGCUACUAAGGUAUGAAGGUGUCUGCGAAAGGUAACGUAAAUCAUUCUCGGCUCCUUGCAAAGUACGACUAGGAUCCAUCGUACACAUCCGGACGAAGAUGUAAAAUUGACGCCCCUGUAGGCCGUGAGACAGACGUGAGCCAAACCAUCUGCUCUACUUCUGGAGGCCUUGAAUAGUGGCGCGUUGUGUAAUCUUAAGAGAGAUUUUACUUGGAAUUACAGCCUACUUUGACCAGUAGCGCAUUGUGAACAAAUAUUCCCGUACGCGUCCAAUUGCAGCAAAACGUGGGCCUGUGUCCAGU
diff -r bd5d779a7a38 -r cab9b21eabf9 test-data/spectrast.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/spectrast.log Mon Dec 14 16:54:59 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 bd5d779a7a38 -r cab9b21eabf9 tools_blacklist.txt
--- a/tools_blacklist.txt Fri Nov 06 20:37:11 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