| Previous changeset 16:01dbaf6a57e0 (2020-11-06) Next changeset 18:f4be248c3d47 (2022-12-01) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms" |
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modified:
ConsensusID.xml generate-foo.sh macros.xml macros_autotest.xml macros_test.xml prepare_test_data_manual.sh readme.md test-data.sh |
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removed:
404-urls.patch OMSSAAdapter.patch PepNovoAdapter.patch filetypes.txt fill_ctd_clargs.py generate.sh hardcoded_params.json tools_blacklist.txt |
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| diff -r 01dbaf6a57e0 -r abffdfee3021 404-urls.patch --- a/404-urls.patch Fri Nov 06 19:49:28 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 @@ - <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> |
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| diff -r 01dbaf6a57e0 -r abffdfee3021 ConsensusID.xml --- a/ConsensusID.xml Fri Nov 06 19:49:28 2020 +0000 +++ b/ConsensusID.xml Mon Feb 22 10:46:10 2021 +0000 |
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| b'@@ -1,7 +1,7 @@\n <?xml version=\'1.0\' encoding=\'UTF-8\'?>\n <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->\n <!--Proposed Tool Section: [ID Processing]-->\n-<tool id="ConsensusID" name="ConsensusID" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">\n+<tool id="ConsensusID" name="ConsensusID" version="@TOOL_VERSION@+galaxy1" profile="20.05">\n <description>Computes a consensus of peptide identifications of several identification engines.</description>\n <macros>\n <token name="@EXECUTABLE@">ConsensusID</token>\n@@ -17,7 +17,8 @@\n \n ## Preprocessing\n mkdir in &&\n-${ \' \'.join(["ln -s \'%s\' \'in/%s.%s\' &&" % (_, re.sub(\'[^\\w\\-_]\', \'_\', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }\n+mkdir ${\' \'.join(["\'in/%s\'" % (i) for i, f in enumerate($in) if f])} && \n+${\' \'.join(["ln -s \'%s\' \'in/%s/%s.%s\' && " % (f, i, re.sub(\'[^\\w\\-_]\', \'_\', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in) if f])}\n mkdir out &&\n \n ## Main program call\n@@ -27,7 +28,7 @@\n python3 \'$__tool_directory__/fill_ctd.py\' \'@EXECUTABLE@.ctd\' \'$args_json\' \'$hardcoded_json\' &&\n @EXECUTABLE@ -ini @EXECUTABLE@.ctd\n -in\n-${\' \'.join(["\'in/%s.%s\'"%(re.sub(\'[^\\w\\-_]\', \'_\', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}\n+${\' \'.join(["\'in/%s/%s.%s\'"%(i, re.sub(\'[^\\w\\-_]\', \'_\', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in) if f])}\n -out\n \'out/output.${in[0].ext}\'\n \n@@ -42,8 +43,8 @@\n </configfiles>\n <inputs>\n <param name="in" argument="-in" type="data" format="consensusxml,featurexml,idxml" multiple="true" optional="false" label="input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>\n- <param name="rt_delta" argument="-rt_delta" type="float" optional="true" min="0.0" value="0.1" label="[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum" help=""/>\n- <param name="mz_delta" argument="-mz_delta" type="float" optional="true" min="0.0" value="0.1" label="[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum" help=""/>\n+ <param name="rt_delta" argument="-rt_delta" type="float" optional="false" min="0.0" value="0.1" label="[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum" help=""/>\n+ <param name="mz_delta" argument="-mz_delta" type="float" optional="false" min="0.0" value="0.1" label="[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum" help=""/>\n <param name="per_spectrum" argument="-per_spectrum" type="boolean" truevalue="true" falsevalue="false" checked="false" label="(only idXML) if set, mapping will be done based on exact matching of originating mzml file and spectrum_ref" help=""/>\n <param name="algorithm" argument="-algorithm" type="select" optional="false" label="Algorithm used for consensus scoring" help="* PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores.. * PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities (\'shared peak count\'). Requires PEPs as scores.. * best: For each peptide ID, use the best score of any search engine as the consensus score. Requires the same score type in all ID runs.. * worst: For each peptide ID, use the worst score of any search engine as the consensus score. Requires the same score type in all ID runs.. * average: For each peptide ID, use the average score of all search engines as the consensus. Requires the same score type in all ID runs.. * ranks: Calculates a consensus score based on the ranks of peptide IDs in the results of different search engines. The final score is in the range (0, 1], with 1 bei'..b'ent="-filter:considered_hits" type="integer" optional="false" min="0" value="0" label="The number of top hits in each ID run that are considered for consensus scoring (\'0\' for all hits)" help=""/>\n+ <param name="min_support" argument="-filter:min_support" type="float" optional="false" min="0.0" max="1.0" value="0.0" label="For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed)" help=""/>\n <param name="count_empty" argument="-filter:count_empty" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Count empty ID runs" help="(i.e. those containing no peptide hit for the current spectrum) when calculating \'min_support\'?"/>\n <param name="keep_old_scores" argument="-filter:keep_old_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if set, keeps the original scores as user params" help=""/>\n </section>\n <section name="PEPIons" title="PEPIons algorithm parameters" help="" expanded="false">\n- <param name="mass_tolerance" argument="-PEPIons:mass_tolerance" type="float" optional="true" min="0.0" value="0.5" label="Maximum difference between fragment masses (in Da) for fragments to be considered \'shared\' between peptides" help=""/>\n- <param name="min_shared" argument="-PEPIons:min_shared" type="integer" optional="true" min="1" value="2" label="The minimal number of \'shared\' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC)" help=""/>\n+ <param name="mass_tolerance" argument="-PEPIons:mass_tolerance" type="float" optional="false" min="0.0" value="0.5" label="Maximum difference between fragment masses (in Da) for fragments to be considered \'shared\' between peptides" help=""/>\n+ <param name="min_shared" argument="-PEPIons:min_shared" type="integer" optional="false" min="1" value="2" label="The minimal number of \'shared\' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC)" help=""/>\n </section>\n <section name="PEPMatrix" title="PEPMatrix algorithm parameters" help="" expanded="false">\n- <param name="matrix" argument="-PEPMatrix:matrix" display="radio" type="select" optional="false" label="Substitution matrix to use for alignment-based similarity scoring" help="">\n+ <param name="matrix" argument="-PEPMatrix:matrix" display="checkboxes" type="select" optional="false" label="Substitution matrix to use for alignment-based similarity scoring" help="">\n <option value="identity" selected="true">identity</option>\n <option value="PAM30MS">PAM30MS</option>\n- <expand macro="list_string_san"/>\n+ <expand macro="list_string_san" name="matrix"/>\n </param>\n- <param name="penalty" argument="-PEPMatrix:penalty" type="integer" optional="true" min="1" value="5" label="Alignment gap penalty (the same value is used for gap opening and extension)" help=""/>\n+ <param name="penalty" argument="-PEPMatrix:penalty" type="integer" optional="false" min="1" value="5" label="Alignment gap penalty (the same value is used for gap opening and extension)" help=""/>\n </section>\n <expand macro="adv_opts_macro">\n <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>\n- <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">\n- <expand macro="list_string_san"/>\n+ <param name="test" argument="-test" type="hidden" optional="false" value="False" label="Enables the test mode (needed for internal use only)" help="">\n+ <expand macro="list_string_san" name="test"/>\n </param>\n </expand>\n <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">\n' |
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| diff -r 01dbaf6a57e0 -r abffdfee3021 OMSSAAdapter.patch --- a/OMSSAAdapter.patch Fri Nov 06 19:49:28 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 && |
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| diff -r 01dbaf6a57e0 -r abffdfee3021 PepNovoAdapter.patch --- a/PepNovoAdapter.patch Fri Nov 06 19:49:28 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 @@ - </configfiles> - <inputs> - <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> -- <param name="model_directory" argument="-model_directory" type="text" optional="false" value="" label="Name of the directory where the model files are kept" help=""> -- <expand macro="list_string_san"/> -+ <param name="model_directory" argument="-model_directory" type="select" optional="false" label="Name of the directory where the model files are kept" help=""> -+ <options from_data_table="pepnovo_models"> -+ <column name="name" index="0"/> -+ <column name="value" index="2"/> -+ <filter type="unique_value" name="unique_set" column="0"/> -+ <validator type="no_options" message="No model directory available"/> -+ </options> - </param> - <param name="correct_pm" argument="-correct_pm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find optimal precursor mass and charge values" help=""/> - <param name="use_spectrum_charge" argument="-use_spectrum_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not correct charge" help=""/> -@@ -51,8 +56,14 @@ - <param name="no_quality_filter" argument="-no_quality_filter" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not remove low quality spectra" help=""/> - <param name="fragment_tolerance" argument="-fragment_tolerance" type="float" optional="true" value="-1.0" label="The fragment tolerance (between 0 and 0.75 Da" help="Set to -1.0 to use model's default setting)"/> - <param name="pm_tolerance" argument="-pm_tolerance" type="float" optional="true" value="-1.0" label="The precursor mass tolerance (between 0 and 5.0 Da" help="Set to -1.0 to use model's default setting)"/> -- <param name="model" argument="-model" type="text" optional="true" value="CID_IT_TRYP" label="Name of the model that should be used" help=""> -- <expand macro="list_string_san"/> -+ <param name="model" argument="-model" type="select" label="Name of the model that should be used" help=""> -+ <options from_data_table="pepnovo_models"> -+ <column name="name" index="1"/> -+ <column name="value" index="1"/> -+ <filter type="param_value" ref="model_directory" column="2"/> -+ <filter type="unique_value" column="1"/> -+ <validator type="no_options" message="No model available"/> -+ </options> - </param> - <param name="digest" argument="-digest" display="radio" type="select" optional="false" label="Enzyme used for digestion (default TRYPSIN)" help=""> - <option value="TRYPSIN" selected="true">TRYPSIN</option> |
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| diff -r 01dbaf6a57e0 -r abffdfee3021 filetypes.txt --- a/filetypes.txt Fri Nov 06 19:49:28 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 |
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| diff -r 01dbaf6a57e0 -r abffdfee3021 fill_ctd_clargs.py --- a/fill_ctd_clargs.py Fri Nov 06 19:49:28 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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()) |
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| diff -r 01dbaf6a57e0 -r abffdfee3021 generate-foo.sh --- a/generate-foo.sh Fri Nov 06 19:49:28 2020 +0000 +++ b/generate-foo.sh Mon Feb 22 10:46:10 2021 +0000 |
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| @@ -83,7 +83,7 @@ #echo python3 fill_ctd_clargs.py --ctd $ini $cli # using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"]) # >&2 echo "python3 fill_ctd_clargs.py --ctd $ini $cli" - eval "python3 fill_ctd_clargs.py --ctd $ini $cli" > "$ctdtmp" + eval "python3 fill_ctd_clargs.py --ini_file $ini --ctd_file ctd/$tool_id.ctd $cli" > "$ctdtmp" # echo $ctdtmp # >&2 cat $ctdtmp testtmp=$(mktemp) |
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| diff -r 01dbaf6a57e0 -r abffdfee3021 generate.sh --- a/generate.sh Fri Nov 06 19:49:28 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 $i.json & -# done |
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| diff -r 01dbaf6a57e0 -r abffdfee3021 hardcoded_params.json --- a/hardcoded_params.json Fri Nov 06 19:49:28 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,236 +0,0 @@ -{ - "#": "blacklist parameters", - - "version": [{"value": "@"}], - "debug": [{"value": "@"}], - "algorithm:debug": [{"value": "@"}], - "java_memory": [{"value": "@"}], - "java_permgen": [{"value": "@"}], - "#": "type of input is always determined from the file extension ", - "in_type": [{"value": "@"}], - - "#": "tool specific blacklist parameters", - - "convert_back": [{"value": "@", "tools": ["OpenSwathMzMLFileCacher"]}], - "NET_executable": [{ - "value": "@", - "tools": ["FileConverter"] - }], - - - "params_file": [{"value": "@", "tools": ["SpectraSTSearchAdapter"]}], - - "#": "TODO not usable in 2.5 https://github.com/OpenMS/OpenMS/issues/4456, corresponding test currently disabled", - "consensus_out": [{"value": "@", "tools": ["MaRaClusterAdapter"]}], - "#": "TODO would need treatment as prefix-output", - "output_directory": [{"value": "@", "tools": ["MaRaClusterAdapter"]}], - - "#": "hardcode parameter values", - - "comet_version": [{ - "value":"2016.01 rev. 3" - }], - "comet_executable": [{ - "value":"comet" - }], - "crux_executable": [{ - "value": "crux" - }], - "fido_executable": [{ - "value":"Fido" - }], - "fidocp_executable": [{ - "value":"FidoChooseParameters" - }], - "maracluster_executable": [{ - "value":"/home/berntm/projects/tools-galaxyp/tools/openms/OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster" - }], - "mascot_directory": [{ - "value":"TODO" - }], - "myrimatch_executable": [{ - "value":"myrimatch" - }], - "omssa_executable": [{ - "value":"$(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"] - - }] -} |
| b |
| diff -r 01dbaf6a57e0 -r abffdfee3021 macros.xml --- a/macros.xml Fri Nov 06 19:49:28 2020 +0000 +++ b/macros.xml Mon Feb 22 10:46:10 2021 +0000 |
| [ |
| @@ -21,6 +21,7 @@ <xml name="stdio"> <stdio> <regex match="std::bad_alloc" level="fatal_oom" description="Could not allocate memory"/> + <regex match="OutOfMemoryError" level="fatal_oom" description="Could not allocate memory"/> <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/> <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/> <regex match="qUncompress: could not allocate enough memory to uncompress data" level="fatal_oom" description="Java memory Exception"/> @@ -45,10 +46,10 @@ </xml> <!-- sanitizers and validators --> - <xml name="list_string_val"> - <validator type="regex" message="parameter must not start with $">^[^$]</validator> + <xml name="list_string_val" token_name=""> + <validator type="regex" message="parameter @NAME@: must not start with $">^[^$]</validator> - <validator type="regex" message="a space separated list of string is needed (strings that contain spaces can be quoted with ")">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator> + <validator type="regex" message="parameter @NAME@: a space separated list of string is needed (strings that contain spaces can be quoted with ")">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator> </xml> <xml name="list_string_san"> <sanitizer> @@ -64,8 +65,8 @@ </valid> </sanitizer> </xml> - <xml name="list_float_valsan"> - <validator type="regex" message="a space separated list of float values is required">^ *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?( *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* *$</validator> + <xml name="list_float_valsan" token_name=""> + <validator type="regex" message="parameter @NAME@: a space separated list of float values is required">^ *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?( *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* *$</validator> <yield/> <sanitizer> <valid initial="string.digits"> @@ -78,8 +79,8 @@ </valid> </sanitizer> </xml> - <xml name="list_integer_valsan"> - <validator type="regex" message="a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator> + <xml name="list_integer_valsan" token_name=""> + <validator type="regex" message="parameter @NAME@: a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator> <yield/> <sanitizer> <valid initial="string.digits"> |
| b |
| diff -r 01dbaf6a57e0 -r abffdfee3021 macros_autotest.xml --- a/macros_autotest.xml Fri Nov 06 19:49:28 2020 +0000 +++ b/macros_autotest.xml Mon Feb 22 10:46:10 2021 +0000 |
| b |
| b'@@ -126,7 +126,6 @@\n <param name="max_transitions" value="3"/>\n <param name="cosine_similarity_threshold" value="0.98"/>\n <param name="transition_threshold" value="5.0"/>\n- <param name="out_workspace_directory" value=""/>\n <section name="deisotoping">\n <param name="use_deisotoper" value="false"/>\n <param name="fragment_tolerance" value="1.0"/>\n@@ -195,7 +194,6 @@\n <param name="max_transitions" value="3"/>\n <param name="cosine_similarity_threshold" value="0.98"/>\n <param name="transition_threshold" value="5.0"/>\n- <param name="out_workspace_directory" value=""/>\n <section name="deisotoping">\n <param name="use_deisotoper" value="false"/>\n <param name="fragment_tolerance" value="1.0"/>\n@@ -264,7 +262,6 @@\n <param name="max_transitions" value="3"/>\n <param name="cosine_similarity_threshold" value="0.98"/>\n <param name="transition_threshold" value="5.0"/>\n- <param name="out_workspace_directory" value=""/>\n <section name="deisotoping">\n <param name="use_deisotoper" value="false"/>\n <param name="fragment_tolerance" value="1.0"/>\n@@ -333,7 +330,6 @@\n <param name="max_transitions" value="3"/>\n <param name="cosine_similarity_threshold" value="0.98"/>\n <param name="transition_threshold" value="5.0"/>\n- <param name="out_workspace_directory" value=""/>\n <section name="deisotoping">\n <param name="use_deisotoper" value="false"/>\n <param name="fragment_tolerance" value="1.0"/>\n@@ -402,7 +398,6 @@\n <param name="max_transitions" value="3"/>\n <param name="cosine_similarity_threshold" value="0.98"/>\n <param name="transition_threshold" value="5.0"/>\n- <param name="out_workspace_directory" value=""/>\n <section name="deisotoping">\n <param name="use_deisotoper" value="false"/>\n <param name="fragment_tolerance" value="1.0"/>\n@@ -471,7 +466,6 @@\n <param name="max_transitions" value="3"/>\n <param name="cosine_similarity_threshold" value="0.98"/>\n <param name="transition_threshold" value="3.0"/>\n- <param name="out_workspace_directory" value=""/>\n <section name="deisotoping">\n <param name="use_deisotoper" value="false"/>\n <param name="fragment_tolerance" value="1.0"/>\n@@ -540,7 +534,6 @@\n <param name="max_transitions" value="3"/>\n <param name="cosine_similarity_threshold" value="0.98"/>\n <param name="transition_threshold" value="3.0"/>\n- <param name="out_workspace_directory" value=""/>\n <section name="deisotoping">\n <param name="use_deisotoper" value="false"/>\n <param name="fragment_tolerance" value="1.0"/>\n@@ -609,7 +602,6 @@\n <param name="max_transitions" value="3"/>\n <param name="cosine_similarity_threshold" value="0.98"/>\n <param name="transition_threshold" value="3.0"/>\n- <param name="out_workspace_directory" value=""/>\n <section name="deisotoping">\n <param name="use_deisotoper" value="false"/>\n <param name="fragment_tolerance" value="1.0"/>\n@@ -678,7 +670,6 @@\n <param name="max_transitions" value="3"/>\n <param name="cosine_similarity_threshold" value="0.98"/>\n <param name="transition_threshold" value="3.0"/>\n- <param name="out_workspace_directory" value=""/>\n <section name="deisotoping">\n <param name="use_deisotoper" value="false"/>\n <param name="fragment_tolerance" value="1.0"/>\n@@ -758,7 +749,6 @@\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="digest_mass_range" value="600:5000"/>\n <param name="max_precursor_charge" value="5"/>\n <param name="spectrum_batch_size" value="1000"/>\n@@ -796,8 +786,8 @@\n <param name="activation_method" value="ALL"/>\n <param n'..b'am name="filter_by_num_masstraces" value="1"/>\n <param name="precursor_mz_tolerance" value="0.005"/>\n@@ -25644,7 +25262,6 @@\n <param name="in" value="SiriusAdapter_4_input.mzML"/>\n <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>\n <output name="out_ms" file="SiriusAdapter_6_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/>\n- <param name="out_workspace_directory" value=""/>\n <section name="preprocessing">\n <param name="filter_by_num_masstraces" value="1"/>\n <param name="precursor_mz_tolerance" value="0.005"/>\n@@ -25687,7 +25304,6 @@\n <param name="in" value="SiriusAdapter_4_input.mzML"/>\n <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>\n <output name="out_sirius" file="SiriusAdapter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>\n- <param name="out_workspace_directory" value=""/>\n <section name="preprocessing">\n <param name="filter_by_num_masstraces" value="1"/>\n <param name="precursor_mz_tolerance" value="0.005"/>\n@@ -25731,7 +25347,6 @@\n <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/>\n <output name="out_sirius" file="SiriusAdapter_4_output.tmp" compare="sim_size" delta="5700" ftype="mztab"/>\n <output name="out_fingerid" file="SiriusAdapter_4_foutput.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>\n- <param name="out_workspace_directory" value=""/>\n <section name="preprocessing">\n <param name="filter_by_num_masstraces" value="1"/>\n <param name="precursor_mz_tolerance" value="0.005"/>\n@@ -25798,8 +25413,6 @@\n <param name="cut_peaks_below" value="1000"/>\n </section>\n <section name="modifications">\n- <param name="fixed" value=""/>\n- <param name="variable" value=""/>\n <param name="variable_max_per_peptide" value="2"/>\n </section>\n <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>\n@@ -27122,7 +26735,7 @@\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="fixed_modifications" value="Carbamidomethyl (C)"/>\n <param name="variable_modifications" value="Oxidation (M)"/>\n <param name="minimum_fragment_mz" value="150.0"/>\n <param name="enzyme" value="Trypsin"/>\n@@ -27154,7 +26767,7 @@\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="fixed_modifications" value="Carbamidomethyl (C)"/>\n <param name="variable_modifications" value="Oxidation (M)"/>\n <param name="minimum_fragment_mz" value="150.0"/>\n <param name="enzyme" value="Trypsin"/>\n@@ -27186,7 +26799,7 @@\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="fixed_modifications" value="Carbamidomethyl (C)"/>\n <param name="variable_modifications" value="Oxidation (M)"/>\n <param name="minimum_fragment_mz" value="150.0"/>\n <param name="enzyme" value="Trypsin"/>\n@@ -27202,4 +26815,4 @@\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+<xml name="autotest_PTPredict"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_InspectAdapter"/><xml name="autotest_RTPredict"/><xml name="autotest_ProteomicsLFQ"/></macros>\n' |
| b |
| diff -r 01dbaf6a57e0 -r abffdfee3021 macros_test.xml --- a/macros_test.xml Fri Nov 06 19:49:28 2020 +0000 +++ b/macros_test.xml Mon Feb 22 10:46:10 2021 +0000 |
| b |
| @@ -127,8 +127,8 @@ <param name="in" value="IDRipper_2_input.idXML"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output_collection name="out_path" count="2"> - <element name="IDRipper_2_output1" file="IDRipper_2_output1.idXML" ftype="idxml"/> - <element name="IDRipper_2_output2" file="IDRipper_2_output2.idXML" ftype="idxml"/> + <element name="IDRipper_2_output_1" file="IDRipper_2_output1.idXML" ftype="idxml"/> + <element name="IDRipper_2_output_2" file="IDRipper_2_output2.idXML" ftype="idxml"/> </output_collection> <output name="ctd_out" ftype="xml"> <assert_contents> @@ -266,17 +266,16 @@ <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> <output_collection name="output_files" count="1"> - <element name="OpenSwathAnalyzer_2_swathfile_mzML.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/> + <element name="OpenSwathAnalyzer_2_swathfile_mzML" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/> </output_collection> </test> - <!-- test with two inputs (actually the same file .. symlinked) --> <test> <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/> <output_collection name="output_files" count="2"> - <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/> - <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/> + <element name="OpenSwathDIAPreScoring_in1_mzML" file="OpenSwathDIAPreScoring_2_1.tsv" ftype="tabular"/> + <element name="OpenSwathDIAPreScoring_in2_mzML" file="OpenSwathDIAPreScoring_2_2.tsv" ftype="tabular"/> </output_collection> </test> </xml> @@ -335,6 +334,7 @@ <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/> </test> </xml> +<!-- TODO PSMFeatureExtractor should have auto tests with 2.7 https://github.com/OpenMS/OpenMS/pull/5087 --> <xml name="manutest_PSMFeatureExtractor"> <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible --> <param name="adv_opts_cond|test" value="true"/> @@ -354,6 +354,13 @@ <param name="out_type" value="mzid"/> <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="500"/> </test> + <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible --> + <param name="adv_opts_cond|test" value="true"/> + <param name="in_single" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/> + <param name="adv_opts_cond|adv_opts_selector" value="advanced"/> + <param name="out_type" value="idxml"/> + <output name="out" ftype="idxml" value="PSMFeatureExtractor_3.idXML" compare="sim_size" delta="500"/> + </test> </xml> <xml name="manutest_QCCalculator"> <test expect_num_outputs="1"><!-- took test data from another test w mzML input --> |
| b |
| diff -r 01dbaf6a57e0 -r abffdfee3021 prepare_test_data_manual.sh --- a/prepare_test_data_manual.sh Fri Nov 06 19:49:28 2020 +0000 +++ b/prepare_test_data_manual.sh Mon Feb 22 10:46:10 2021 +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 |
| b |
| diff -r 01dbaf6a57e0 -r abffdfee3021 readme.md --- a/readme.md Fri Nov 06 19:49:28 2020 +0000 +++ b/readme.md Mon Feb 22 10:46:10 2021 +0000 |
| b |
| @@ -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 @@ -71,10 +74,15 @@ Preprocessing: -- For each input / output data set parameter a directory is crated (named by - the parameter) - For input data set parameters the links to the actual location of the data - sets are created + sets are created, the link names are `element_identifier`.`EXT`, where `EXT` + is an extension that is known by OpenMS +- In order to avoid name collisions for the created links each is placed in a + unique directory: `PARAM_NAME/DATASET_ID`, where `PARAM_NAME` is the name + of the parameter and `DATASET_ID` is the id of the Galaxy dataset +- the same happens for output parameters that are in 1:1 correspondence with + an input parameter + Main: |
| b |
| diff -r 01dbaf6a57e0 -r abffdfee3021 test-data.sh --- a/test-data.sh Fri Nov 06 19:49:28 2020 +0000 +++ b/test-data.sh Mon Feb 22 10:46:10 2021 +0000 |
| [ |
| @@ -15,8 +15,11 @@ export OPENMSGIT="$tmp/OpenMS$VERSION.0-git" export OPENMSPKG="$tmp/OpenMS$VERSION-pkg/" -export OPENMSENV="$tmp/OpenMS$VERSION-env" -export CTDCONVERTER="$tmp/CTDConverter" +export OPENMSENV="OpenMS$VERSION-env" + +if [ -z "$CTDCONVERTER" ]; then + export CTDCONVERTER="$tmp/CTDConverter" +fi if [[ -z "$1" ]]; then autotests="/dev/null" @@ -59,7 +62,7 @@ if conda env list | grep "$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 ctdopts=1.4 lxml + conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -n $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION ctdopts=1.4 lxml # chmod -R u-w $OPENMSENV fi ############################################################################### @@ -82,10 +85,10 @@ echo "Clone CTDConverter" 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 + git clone -b topic/fix-selects https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER else cd $CTDCONVERTER - git pull origin topic/cdata + git pull origin topic/fix-selects cd - fi @@ -185,17 +188,17 @@ prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh -# prepare_test_data > tmp_test_data.sh -# # remove calls not needed for the tools listed in any .list file -# echo LIST $LIST -# if [ ! -z "$LIST" ]; then -# REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//') -# else -# REX=".*" -# fi -# echo REX $REX -# cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh -# rm tmp_test_data.sh +## prepare_test_data > tmp_test_data.sh +## # remove calls not needed for the tools listed in any .list file +## echo LIST $LIST +## if [ ! -z "$LIST" ]; then +## REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//') +## else +## REX=".*" +## fi +## echo REX $REX +## cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh +## rm tmp_test_data.sh echo "Execute test shell script" chmod u+x prepare_test_data.sh |
| b |
| diff -r 01dbaf6a57e0 -r abffdfee3021 tools_blacklist.txt --- a/tools_blacklist.txt Fri Nov 06 19:49:28 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -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 |