| Previous changeset 9:047020d9012f (2021-01-30) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 |
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modified:
PSMFeatureExtractor.xml fill_ctd.py generate-foo.sh macros.xml readme.md test-data.sh |
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added:
fill_ctd_clargs.py |
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removed:
macros_autotest.xml macros_discarded_auto.xml macros_test.xml |
| b |
| diff -r 047020d9012f -r 63fea23042c4 PSMFeatureExtractor.xml --- a/PSMFeatureExtractor.xml Sat Jan 30 11:38:47 2021 +0000 +++ b/PSMFeatureExtractor.xml Thu Dec 01 19:01:06 2022 +0000 |
| [ |
| b'@@ -1,13 +1,11 @@\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: [Utilities]-->\n-<tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="@TOOL_VERSION@+galaxy2" profile="20.05">\n+<tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">\n <description>Computes extra features for each input PSM.</description>\n <macros>\n <token name="@EXECUTABLE@">PSMFeatureExtractor</token>\n <import>macros.xml</import>\n- <import>macros_autotest.xml</import>\n- <import>macros_test.xml</import>\n </macros>\n <expand macro="requirements"/>\n <expand macro="stdio"/>\n@@ -16,11 +14,12 @@\n #import re\n \n ## Preprocessing\n-mkdir in &&\n-#if $in\n-${ \' \'.join(["ln -s \'%s\' \'in/%s.%s\' &&" % (_, re.sub(\'[^\\w\\-_]\', \'_\', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }\n-#else if $in_single\n- ln -s \'$in_single\' \'in/${re.sub("[^\\w\\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)\' && \n+mkdir in_cond.in &&\n+#if $in_cond.in_select == "no"\n+mkdir ${\' \'.join(["\'in_cond.in/%s\'" % (i) for i, f in enumerate($in_cond.in) if f])} && \n+${\' \'.join(["ln -s \'%s\' \'in_cond.in/%s/%s.%s\' && " % (f, i, re.sub(\'[^\\w\\-_]\', \'_\', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}\n+#else\n+ln -s \'$in_cond.in\' \'in_cond.in/${re.sub("[^\\w\\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)\' &&\n #end if\n mkdir out &&\n \n@@ -31,10 +30,10 @@\n python3 \'$__tool_directory__/fill_ctd.py\' \'@EXECUTABLE@.ctd\' \'$args_json\' \'$hardcoded_json\' &&\n @EXECUTABLE@ -ini @EXECUTABLE@.ctd\n -in\n-#if $in\n-${\' \'.join(["\'in/%s.%s\'"%(re.sub(\'[^\\w\\-_]\', \'_\', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}\n-#else if $in_single\n-\'in/${re.sub("[^\\w\\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)\'\n+#if $in_cond.in_select == "no"\n+${\' \'.join(["\'in_cond.in/%s/%s.%s\'"%(i, re.sub(\'[^\\w\\-_]\', \'_\', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}\n+#else\n+\'in_cond.in/${re.sub("[^\\w\\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)\'\n #end if\n -out\n \'out/output.${out_type}\'\n@@ -49,26 +48,36 @@\n <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>\n </configfiles>\n <inputs>\n- <param name="in_single" argument="-in" type="data" format="idxml,mzid" multiple="false" optional="true" label="Input file for batch processing" help="(exactly one of -in or -in_list is required)"/>\n- <param name="in" argument="-in" type="data" format="idxml,mzid" multiple="true" optional="true" label="Input file(s) for joint processing" help="(exactly one of -in or -in_list is required)"/> \n- <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">\n+ <conditional name="in_cond">\n+ <param name="in_select" type="select" label="Run tool in batch mode for -in">\n+ <option value="no">No: process all datasets jointly</option>\n+ <option value="yes">Yes: process each dataset in an independent job</option>\n+ </param>\n+ <when value="no">\n+ <param argument="-in" type="data" format="idxml,mzid" multiple="true" optional="false" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>\n+ </when>\n+ <when value="yes">\n+ <param argument="-in" type="data" format="idxml,mzid" multiple="false" optional="false" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>\n+ </when>\n+ </conditional>\n+ <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined fr'..b'+ <param argument="-concat" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Naive merging of PSMs from different search engines: concatenate multiple search results instead of merging on scan level" help="Only valid together with -multiple_search_engines flag"/>\n+ <param argument="-impute" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Will instead of discarding all PSM not unanimously detected by all SE, impute missing values by their respective scores min/max observed" help="Only valid together with -multiple_search_engines flag"/>\n+ <param argument="-limit_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Will impute missing scores with the worst numerical limit (instead of min/max observed) of the respective score" help="Only valid together with -multiple_search_engines flag"/>\n+ <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>\n+ <param 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" name="test"/>\n </param>\n </expand>\n <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">\n@@ -76,9 +85,8 @@\n </param>\n </inputs>\n <outputs>\n- <data name="out" label="${tool.name} on ${on_string}: out">\n+ <data name="out" label="${tool.name} on ${on_string}: out" format="idxml">\n <change_format>\n- <when input="out_type" value="idXML" format="idxml"/>\n <when input="out_type" value="mzid" format="mzid"/>\n </change_format>\n </data>\n@@ -86,13 +94,34 @@\n <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>\n </data>\n </outputs>\n- <tests>\n- <expand macro="autotest_PSMFeatureExtractor"/>\n- <expand macro="manutest_PSMFeatureExtractor"/>\n- </tests>\n+ <tests><test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->\n+ <param name="adv_opts|test" value="true"/>\n+ <param name="adv_opts|skip_db_check" value="true"/>\n+ <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>\n+ <param name="multiple_search_engines" value="true"/>\n+ <param name="out_type" value="idxml"/>\n+ <output name="out" ftype="idxml" value="PSMFeatureExtractor.idxml" compare="sim_size" delta="500"/>\n+ </test>\n+ <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->\n+ <param name="adv_opts|test" value="true"/>\n+ <param name="adv_opts|skip_db_check" value="true"/>\n+ <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>\n+ <param name="multiple_search_engines" value="true"/>\n+ <param name="out_type" value="mzid"/>\n+ <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="500"/>\n+ </test>\n+ <!-- test for the batch conditional crated for data parameters with multiple="true" -->\n+ <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->\n+ <param name="adv_opts|test" value="true"/>\n+ <param name="in_select" value="yes"/>\n+ <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>\n+ <param name="out_type" value="idxml"/>\n+ <output name="out" ftype="idxml" value="PSMFeatureExtractor_3.idXML" compare="sim_size" delta="500"/>\n+ </test>\n+</tests>\n <help><![CDATA[Computes extra features for each input PSM.\n \n \n-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_PSMFeatureExtractor.html]]></help>\n+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_PSMFeatureExtractor.html]]></help>\n <expand macro="references"/>\n </tool>\n' |
| b |
| diff -r 047020d9012f -r 63fea23042c4 fill_ctd.py --- a/fill_ctd.py Sat Jan 30 11:38:47 2021 +0000 +++ b/fill_ctd.py Thu Dec 01 19:01:06 2022 +0000 |
| [ |
| @@ -32,7 +32,7 @@ for k, v in e.items(): if (k in d and isinstance(d[k], dict) and isinstance(e[k], collections.abc.Mapping)): mergeDicts(d[k], e[k]) - elif k not in d and not isinstance(e[k], collections.abc.Mapping): + elif k not in d: d[k] = e[k] else: sys.stderr.write("fill_ctd.py: could not merge key %s for %s in %s" % (k, d, e)) @@ -135,9 +135,10 @@ # insert the hc_args into the args mergeDicts(args, hc_args) -if "adv_opts_cond" in args: - args.update(args["adv_opts_cond"]) - del args["adv_opts_cond"] +# put the contents of the advanced options section into the main dict +if "adv_opts" in args: + args.update(args["adv_opts"]) + del args["adv_opts"] # 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" |
| b |
| diff -r 047020d9012f -r 63fea23042c4 fill_ctd_clargs.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fill_ctd_clargs.py Thu Dec 01 19:01:06 2022 +0000 |
| [ |
| @@ -0,0 +1,70 @@ +#!/usr/bin/env python3 + +import operator +from argparse import ArgumentParser +from functools import reduce # forward compatibility for Python 3 +from io import StringIO + +from CTDopts.CTDopts import ( + _Null, + CTDModel, + ModelTypeError, + Parameters +) + + +def getFromDict(dataDict, mapList): + return reduce(operator.getitem, mapList, dataDict) + + +def setInDict(dataDict, mapList, value): + getFromDict(dataDict, mapList[:-1])[mapList[-1]] = value + + +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 stdout", + add_help=False, allow_abbrev=False) + parser.add_argument("--ini_file", dest="ini_file", help="input ini file", + metavar='INI', default=None, required=True) + parser.add_argument("--ctd_file", dest="ctd_file", help="input ctd file" + "if given then optional parameters from the ini file" + "will be filled with the defaults from this CTD file", + metavar='CTD', default=None, required=False) + args, cliargs = parser.parse_known_args() + + # load CTDModel + ini_model = None + try: + ini_model = CTDModel(from_file=args.ini_file) + except ModelTypeError: + pass + try: + ini_model = Parameters(from_file=args.ini_file) + except ModelTypeError: + pass + assert ini_model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ini_file) + + # get a dictionary of the ctd arguments where the values of the parameters + # given on the command line are overwritten + ini_values = ini_model.parse_cl_args(cl_args=cliargs, ignore_required=True) + + if args.ctd_file: + ctd_model = CTDModel(from_file=args.ctd_file) + ctd_values = ctd_model.get_defaults() + for param in ini_model.get_parameters(): + if not param.required and (param.default is None or type(param.default) is _Null): + lineage = param.get_lineage(name_only=True) + try: + default = getFromDict(ctd_values, lineage) + except KeyError: + continue + setInDict(ini_values, lineage, default) + + # write the ctd with the values taken from the dictionary + out = StringIO() + ctd_tree = ini_model.write_ctd(out, ini_values) + print(out.getvalue()) |
| b |
| diff -r 047020d9012f -r 63fea23042c4 generate-foo.sh --- a/generate-foo.sh Sat Jan 30 11:38:47 2021 +0000 +++ b/generate-foo.sh Thu Dec 01 19:01:06 2022 +0000 |
| [ |
| b'@@ -8,17 +8,15 @@\n \n # get the tests from the CMakeLists.txt\n # 1st remove some tests\n- # - OpenSwathMzMLFileCacher with -convert_back argumen https://github.com/OpenMS/OpenMS/issues/4399\n+ # - OpenSwathMzMLFileCacher with -convert_back argument https://github.com/OpenMS/OpenMS/issues/4399\n # - IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differentlt\n # - several tools with duplicated input (leads to conflict when linking)\n- # - TOFCalibration inputs we extension (also in prepare_test_data) https://github.com/OpenMS/OpenMS/pull/4525\n # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456)\n # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed)\n # - some input files are originally in a subdir (degenerated cases/), but not in test-data\n- # - SeedListGenerator: https://github.com/OpenMS/OpenMS/issues/4404\n # - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet)\n- # - FeatureFinderIdentification name clash of two tests https://github.com/OpenMS/OpenMS/pull/5002\n- # - TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010\n+ # - SiriusAdapter_4 depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010\n+ # - SiriusAdapter_10 should work in >2.8 https://github.com/OpenMS/OpenMS/issues/5869\n CMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake |\n sed \'s@${DATA_DIR_SHARE}/@@g\' |\n grep -v \'OpenSwathMzMLFileCacher .*-convert_back\' |\n@@ -26,19 +24,9 @@\n grep -v "MaRaClusterAdapter.*-consensus_out"|\n grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " |\n sed \'s@degenerate_cases/@@g\' |\n- grep -v \'TOPP_SeedListGenerator_3"\' | \n egrep -v \'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"\' |\n-\tegrep -v \'"TOPP_FeatureFinderIdentification_4"\' | \n-\tsed \'s/\\("TOPP_SiriusAdapter_4".*\\)-sirius:database all\\(.*\\)/\\1-sirius:database pubchem\\2/\')\n-\n-\n-# grep -v \'FileFilter.*-spectra:select_polarity ""\' |\n-# grep -v \'MassTraceExtractor_2.ini \' |\n-# grep -v "FileMerger_6_input2.mzML.*FileMerger_6_input2.mzML" |\n-# grep -v "IDMerger_1_input1.idXML.*IDMerger_1_input1.idXML" |\n-# grep -v "degenerated_empty.idXML.*degenerated_empty.idXML" |\n-# grep -v "FeatureLinkerUnlabeledKD_1_output.consensusXML.*FeatureLinkerUnlabeledKD_1_output.consensusXML" |\n-# grep -v "FeatureLinkerUnlabeledQT_1_output.consensusXML.*FeatureLinkerUnlabeledQT_1_output.consensusXML" |\n+ sed \'s/\\("TOPP_SiriusAdapter_4".*\\)-sirius:database all\\(.*\\)/\\1-sirius:database pubchem\\2/\' |\n+ grep -v \'"TOPP_SiriusAdapter_10"\')\n \n # 1st part is a dirty hack to join lines containing a single function call, e.g.\n # addtest(....\n@@ -50,6 +38,7 @@\n # >&2 echo $line\n test_id=$(echo "$line" | cut -d" " -f 1)\n tool_id=$(echo "$line" | cut -d" " -f 2)\n+ # >&2 echo "test_id $test_id"\n if [[ $test_id =~ _out_?[0-9]? ]]; then\n >&2 echo " skip $test_id $line"\n continue\n@@ -67,7 +56,7 @@\n tes=" <test>\\n"\n line=$(fix_tmp_files "$line")\n line=$(unique_files "$line")\n- # >&2 echo $line\n+ # >&2 echo LINE $line\n #if there is an ini file then we use this to generate the test\n #otherwise the ctd file is used\n #other command line parameters are inserted later into this xml\n@@ -77,19 +66,23 @@\n else\n ini="ctd/$tool_id.ctd"\n fi\n+ # >&2 echo "========================================================"\n+ # >&2 echo "USING ini $ini"\n cli=$(echo $line |cut -d" " -f3- | sed \'s/-ini [^ ]\\+//\')\n \n ctdtmp=$(mktemp)\n- #echo python3 fill_ctd_clargs.py --ctd $ini $cli\n'..b'SION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib > /dev/null\n+ # >&2 echo CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7"\n+ CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7" > /dev/null\n+ echo "<!-- $test_id -->"\n cat $testtmp | grep -v \'<output.*file=""\' # | grep -v \'CHEMISTRY/\'\n- rm $ctdtmp $testtmp\n+\n+ rm "$ctdtmp" "$testtmp"\n \n #> /dev/null\n \n@@ -130,23 +123,23 @@\n #(e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt)\n #this function replaces the tmp file by the expected file. \n function fix_tmp_files {\n-# >&2 echo "FIX $line"\n+ # >&2 echo "FIX $line"\n ret=""\n for a in $@; do\n- if [[ ! $a =~ .tmp$ ]]; then\n+ # >&2 echo " a "$a\n+ if [[ ! $a =~ .tmp$ ]] && [[ ! $a =~ _tmp_ ]]; then\n ret="$ret $a"\n continue\n fi\n-# >&2 echo " a "$a\n- g=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | awk \'{printf("%s@NEWLINE@", $0)}\' | sed \'s/)@NEWLINE@/)\\n/g\' | sed \'s/@NEWLINE@/ /g\' | grep \'\\${DIFF}.*\'"$a")\n-# >&2 echo " g "$g\n- in1=$(sed \'s/.*-in1 \\([^ ]\\+\\).*/\\1/\' <<<$g)\n+ diff_line=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | awk \'{printf("%s@NEWLINE@", $0)}\' | sed \'s/)@NEWLINE@/)\\n/g\' | sed \'s/@NEWLINE@/ /g\' | grep \'\\${DIFF}.*\'"$a")\n+ # >&2 echo " diff_line "$diff_line\n+ in1=$(sed \'s/.*-in1 \\([^ ]\\+\\).*/\\1/\' <<<$diff_line)\n # >&2 echo " in1 "$in1\n if [[ "$a" != "$in1" ]]; then\n ret="$ret $a"\n continue\n fi\n- in2=$(sed \'s/.*-in2 \\([^ ]\\+\\).*/\\1/\' <<<$g)\n+ in2=$(sed \'s/.*-in2 \\([^ ]\\+\\).*/\\1/\' <<<$diff_line)\n in2=$(basename $in2 | sed \'s/)$//\')\n # >&2 echo " in2 "$in2\n if [[ -f "test-data/$in2" ]]; then\n@@ -176,11 +169,11 @@\n fi\n ln -f -s $in1 test-data/$in2\n done\n- for i in test-data/*.tmp\n- do\n+ \n+ find test-data/ -name "*.tmp" -print0 | \n+ while IFS= read -r -d \'\' i; do \n if [ ! -e test-data/$(basename $i .tmp) ]; then\n ln -s $(basename $i) test-data/$(basename $i .tmp)\n- #ln -s $(basename $i) test-data/$(basename $i .tmp)\n else\n ln -fs $(basename $i) test-data/$(basename $i .tmp)\n fi\n@@ -194,14 +187,14 @@\n # id=$1\n # | egrep -i "$id\\_.*[0-9]+(_prepare\\"|_convert)?"\n \n-# TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010\n+ # TODO SiriusAdapter depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010\n cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed \'s/#.*$//\'| sed \'s/^\\s*//; s/\\s*$//\' | grep -v "^$" | awk \'{printf("%s@NEWLINE@", $0)}\' | sed \'s/)@NEWLINE@/)\\n/g\' | sed \'s/@NEWLINE@/ /g\' | \n sed \'s/degenerate_cases\\///\' | \n egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | \n grep add_test | \n egrep "TOPP|UTILS" |\n sed \'s@${DATA_DIR_SHARE}/@@g;\'|\n- sed \'s@${TMP_RIP_PATH}@dummy2.tmp@g\'|\n+ sed \'s@${TMP_RIP_PATH}@./@g\'|\n sed \'s@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @\'| \n \tsed \'s/\\("TOPP_SiriusAdapter_4".*\\)-sirius:database all\\(.*\\)/\\1-sirius:database pubchem\\2/\' |\n while read line\n' |
| b |
| diff -r 047020d9012f -r 63fea23042c4 macros.xml --- a/macros.xml Sat Jan 30 11:38:47 2021 +0000 +++ b/macros.xml Thu Dec 01 19:01:06 2022 +0000 |
| [ |
| @@ -3,14 +3,15 @@ You can edit this file to add your own macros, if you so desire, or you can add additional macro files using the m/macros parameter --> <macros> - <token name="@TOOL_VERSION@">2.6</token> - <token name="@GALAXY_VERSION@">0</token> + <token name="@TOOL_VERSION@">2.8</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">openms</requirement> <requirement type="package" version="@TOOL_VERSION@">openms-thirdparty</requirement> - <!-- makeblastdb for OMSSAAdapter --> - <requirement type="package" version="2.9.0">blast</requirement> + <!-- omssa (which has been excluded from 3rdparty) and makeblastdb for OMSSAAdapter --> + <requirement type="package" version="2.1.9">omssa</requirement> + <requirement type="package" version="2.13.0">blast</requirement> <!--<requirement type="package" version="5.0.0">tpp</requirement>--> <!-- for realpath (used e.g. in LuciphorAdapter) --> <!--<requirement type="package" version="8.25">coreutils</requirement>--> @@ -33,23 +34,15 @@ </citations> </xml> <xml name="adv_opts_macro"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic"/> - <when value="advanced"> - <yield/> - </when> - </conditional> + <section name="adv_opts" title="Advanced Options" expanded="false"> + <yield/> + </section> </xml> <!-- sanitizers and validators --> - <xml name="list_string_val"> - <validator type="regex" message="parameter 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> + <xml name="list_string_val" token_name=""> + <validator type="regex" message="parameter @NAME@: must not start with $">^[^$]</validator> + <validator type="regex" message="parameter @NAME@: a space separated list of string is needed (strings that contain spaces can be quoted with ")">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator> </xml> <xml name="list_string_san"> <sanitizer> @@ -65,8 +58,8 @@ </valid> </sanitizer> </xml> - <xml name="list_float_valsan"> - <validator type="regex" message="a space separated list of float values is required">^ *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?( *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* *$</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]+)?)* *$</validator> <yield/> <sanitizer> <valid initial="string.digits"> @@ -79,8 +72,8 @@ </valid> </sanitizer> </xml> - <xml name="list_integer_valsan"> - <validator type="regex" message="a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</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"> @@ -120,11 +113,11 @@ </token> <token name="@EXT_FOO@"><![CDATA[#def oms2gxyext(o) - #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'} + #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzQC': 'mzqc', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'oms': 'sqlite', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'} #return m[o] #end def #def gxy2omsext(g) - #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'} + #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mzqc': 'mzQC', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'sqlite': 'oms', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'} #return m[g] #end def ]]></token></macros> |
| b |
| diff -r 047020d9012f -r 63fea23042c4 macros_autotest.xml --- a/macros_autotest.xml Sat Jan 30 11:38:47 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,27189 +0,0 @@\n-<?xml version=\'1.0\' encoding=\'UTF-8\'?>\n-<macros>\n- <xml name="autotest_AccurateMassSearch">\n- <test expect_num_outputs="2">\n- <conditional name="adv_opts_cond">\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="force" value="false"/>\n- <param name="test" value="true"/>\n- </conditional>\n- <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/>\n- <output name="out" file="AccurateMassSearch_1_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>\n- <param name="positive_adducts" value="CHEMISTRY/PositiveAdducts.tsv" ftype="tabular"/>\n- <param name="negative_adducts" value="CHEMISTRY/NegativeAdducts.tsv" ftype="tabular"/>\n- <section name="db">\n- <param name="mapping" value="CHEMISTRY/HMDBMappingFile.tsv" ftype="tabular"/>\n- <param name="struct" value="CHEMISTRY/HMDB2StructMapping.tsv" ftype="tabular"/>\n- </section>\n- <section name="algorithm">\n- <param name="mass_error_value" value="5.0"/>\n- <param name="mass_error_unit" value="ppm"/>\n- <param name="ionization_mode" value="positive"/>\n- <param name="isotopic_similarity" value="false"/>\n- <param name="use_feature_adducts" value="false"/>\n- <param name="keep_unidentified_masses" value="false"/>\n- <section name="mzTab">\n- <param name="exportIsotopeIntensities" value="false"/>\n- </section>\n- </section>\n- <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>\n- <output name="ctd_out" ftype="xml">\n- <assert_contents>\n- <is_valid_xml/>\n- </assert_contents>\n- </output>\n- </test>\n- <test expect_num_outputs="3">\n- <conditional name="adv_opts_cond">\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="force" value="false"/>\n- <param name="test" value="true"/>\n- </conditional>\n- <param name="in" value="AccurateMassSearch_2_input.featureXML"/>\n- <output name="out" file="AccurateMassSearch_2_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>\n- <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>\n- <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>\n- <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>\n- <section name="db">\n- <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/>\n- <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/>\n- </section>\n- <section name="algorithm">\n- <param name="mass_error_value" value="5.0"/>\n- <param name="mass_error_unit" value="ppm"/>\n- <param name="ionization_mode" value="positive"/>\n- <param name="isotopic_similarity" value="false"/>\n- <param name="use_feature_adducts" value="false"/>\n- <param name="keep_unidentified_masses" value="false"/>\n- <section name="mzTab">\n- <param name="exportIsotopeIntensities" value="true"/>\n- </section>\n- </section>\n- <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/>\n- <output name="ctd_out" ftype="xml">\n- <assert_contents>\n- <is_valid_xml/>\n- </assert_contents>\n- </output>\n- </test>\n- <test expect_num_outputs="3">\n- <conditional name="adv_opts_cond">\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="force" value="false"/>\n- <param name="test" value="true"/>\n- </conditional>\n- <param name="in" value="AccurateMassSearch_2_input.featureXML"/>\n- <output name="out" file="AccurateMassSearch_3_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>\n- <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>\n- <param name'..b' value="Oxidation (M)"/>\n- <param name="minimum_fragment_mz" value="150.0"/>\n- <param name="enzyme" value="Trypsin"/>\n- <param name="missed_cleavages" value="1"/>\n- <param name="semi_cleavage" value="false"/>\n- <param name="output_results" value="all"/>\n- <param name="max_valid_expect" value="0.1"/>\n- <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>\n- <output name="ctd_out" ftype="xml">\n- <assert_contents>\n- <is_valid_xml/>\n- </assert_contents>\n- </output>\n- </test>\n- <test expect_num_outputs="2">\n- <conditional name="adv_opts_cond">\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="force" value="false"/>\n- <param name="test" value="true"/>\n- </conditional>\n- <param name="in" value="spectra.mzML"/>\n- <output name="out" file="XTandemAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>\n- <param name="database" value="proteins.fasta"/>\n- <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/>\n- <param name="ignore_adapter_param" value="false"/>\n- <param name="precursor_mass_tolerance" value="5.0"/>\n- <param name="fragment_mass_tolerance" value="0.3"/>\n- <param name="precursor_error_units" value="ppm"/>\n- <param name="fragment_error_units" value="Da"/>\n- <param name="max_precursor_charge" value="0"/>\n- <param name="no_isotope_error" value="false"/>\n- <param name="fixed_modifications" value=""/>\n- <param name="variable_modifications" value="Oxidation (M)"/>\n- <param name="minimum_fragment_mz" value="150.0"/>\n- <param name="enzyme" value="Trypsin"/>\n- <param name="missed_cleavages" value="1"/>\n- <param name="semi_cleavage" value="false"/>\n- <param name="output_results" value="valid"/>\n- <param name="max_valid_expect" value="1e-14"/>\n- <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>\n- <output name="ctd_out" ftype="xml">\n- <assert_contents>\n- <is_valid_xml/>\n- </assert_contents>\n- </output>\n- </test>\n- <test expect_num_outputs="2">\n- <conditional name="adv_opts_cond">\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="force" value="false"/>\n- <param name="test" value="true"/>\n- </conditional>\n- <param name="in" value="spectra.mzML"/>\n- <output name="out" file="XTandemAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>\n- <param name="database" value="proteinslong.fasta"/>\n- <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/>\n- <param name="ignore_adapter_param" value="false"/>\n- <param name="precursor_mass_tolerance" value="5.0"/>\n- <param name="fragment_mass_tolerance" value="0.3"/>\n- <param name="precursor_error_units" value="ppm"/>\n- <param name="fragment_error_units" value="Da"/>\n- <param name="max_precursor_charge" value="0"/>\n- <param name="no_isotope_error" value="false"/>\n- <param name="fixed_modifications" value=""/>\n- <param name="variable_modifications" value="Oxidation (M)"/>\n- <param name="minimum_fragment_mz" value="150.0"/>\n- <param name="enzyme" value="Trypsin"/>\n- <param name="missed_cleavages" value="1"/>\n- <param name="semi_cleavage" value="false"/>\n- <param name="output_results" value="all"/>\n- <param name="max_valid_expect" value="0.1"/>\n- <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>\n- <output name="ctd_out" ftype="xml">\n- <assert_contents>\n- <is_valid_xml/>\n- </assert_contents>\n- </output>\n- </test>\n- </xml>\n-<xml name="autotest_InspectAdapter"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_RTPredict"/><xml name="autotest_PTPredict"/><xml name="autotest_IDDecoyProbability"/></macros>\n' |
| b |
| diff -r 047020d9012f -r 63fea23042c4 macros_discarded_auto.xml --- a/macros_discarded_auto.xml Sat Jan 30 11:38:47 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,378 +0,0 @@\n-\n-<xml name="manutest_OpenSwathFileSplitter">\n-<test expect_num_outputs="2">\n- <conditional name="adv_opts_cond">\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="force" value="false"/>\n- <param name="test" value="true"/>\n- </conditional>\n- <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>\n- <output_collection name="outputDirectory" count=""/>\n- <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>\n- <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_qc_FLAG"/>\n- <output name="ctd_out" ftype="xml">\n- <assert_contents>\n- <is_valid_xml/>\n- </assert_contents>\n- </output>\n-</test></xml>\n-<xml name="manutest_IDRipper">\n-<test expect_num_outputs="1">\n- <conditional name="adv_opts_cond">\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="force" value="false"/>\n- <param name="test" value="true"/>\n- </conditional>\n- <param name="in" value="IDRipper_1_input.idXML"/>\n- <output_collection name="out_path" count=""/>\n- <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>\n- <output name="ctd_out" ftype="xml">\n- <assert_contents>\n- <is_valid_xml/>\n- </assert_contents>\n- </output>\n- </test><test expect_num_outputs="1">\n- <conditional name="adv_opts_cond">\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="force" value="false"/>\n- <param name="test" value="true"/>\n- </conditional>\n- <param name="in" value="IDRipper_2_input.idXML"/>\n- <output_collection name="out_path" count=""/>\n- <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>\n- <output name="ctd_out" ftype="xml">\n- <assert_contents>\n- <is_valid_xml/>\n- </assert_contents>\n- </output>\n- </test><test expect_num_outputs="1">\n- <conditional name="adv_opts_cond">\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="force" value="false"/>\n- <param name="test" value="true"/>\n- </conditional>\n- <param name="in" value="IDRipper_3_output.idXML"/>\n- <output_collection name="out_path" count=""/>\n- <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>\n- <output name="ctd_out" ftype="xml">\n- <assert_contents>\n- <is_valid_xml/>\n- </assert_contents>\n- </output>\n- </test></xml>\n-<xml name="manutest_MzMLSplitter">\n-<test expect_num_outputs="1">\n- <conditional name="adv_opts_cond">\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="force" value="false"/>\n- <param name="test" value="true"/>\n- </conditional>\n- <param name="in" value="FileFilter_1_input.mzML"/>\n- <output_collection name="out" count=""/>\n- <param name="parts" value="2"/>\n- <param name="size" value="0"/>\n- <param name="unit" value="MB"/>\n- <param name="no_chrom" value="false"/>\n- <param name="no_spec" value="false"/>\n- <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>\n- <output name="ctd_out" ftype="xml">\n- <assert_contents>\n- <is_valid_xml/>\n- </assert_contents>\n- </output>\n- </test><test expect_num_outputs="1">\n- <conditional name="adv_opts_cond">\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="force" value="false"/>\n- <param name="test" value="true"/>\n- </conditional>\n- <param name="in" value="FileFilter_1_input.mzML"/>\n- <output_collection name="out" count=""/>\n- <param name="parts" value="1"/>\n- <param name="size" value="40"/>\n- <param name="unit" value="KB"/>\n- <param name="no_chrom" value="false"/>\n- <param name="no_spec" value="false"/>\n- <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>\n- <output name="ctd_out" ftype="xml">\n- <assert_contents>\n- <is_valid_xml/>\n- </assert'..b'" value="2"/>\n- <param name="precursor_tolerance" value="20.0"/>\n- <param name="precursor_tolerance_units" value="ppm"/>\n- <param name="force" value="false"/>\n- <param name="test" value="true"/>\n- </conditional>\n- <param name="in" value="MaRaClusterAdapter_1_in_1.mzML,MaRaClusterAdapter_1_in_2.mzML"/>\n- <param name="id_in" value="MaRaClusterAdapter_1_in_3.idXML"/>\n- <output name="out" file="MaRaClusterAdapter_2_out_1.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>\n- <param name="pcut" value="-10.0"/>\n- <param name="min_cluster_size" value="1"/>\n- <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>\n- <output name="ctd_out" ftype="xml">\n- <assert_contents>\n- <is_valid_xml/>\n- </assert_contents>\n- </output>\n- </test></xml>\n-<xml name="manutest_NovorAdapter">\n-<test expect_num_outputs="2">\n- <conditional name="adv_opts_cond">\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="force" value="false"/>\n- <param name="test" value="true"/>\n- </conditional>\n- <param name="in" value="NovorAdapter_in.mzML"/>\n- <output name="out" file="NovorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>\n- <param name="enzyme" value="Trypsin"/>\n- <param name="fragmentation" value="CID"/>\n- <param name="massAnalyzer" value="Trap"/>\n- <param name="fragment_mass_tolerance" value="0.5"/>\n- <param name="precursor_mass_tolerance" value="15.0"/>\n- <param name="precursor_error_units" value="ppm"/>\n- <param name="variable_modifications" value="Acetyl (K)"/>\n- <param name="fixed_modifications" value="Carbamidomethyl (C)"/>\n- <param name="forbiddenResidues" value="I"/>\n- <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>\n- <output name="ctd_out" ftype="xml">\n- <assert_contents>\n- <is_valid_xml/>\n- </assert_contents>\n- </output>\n- </test></xml>\n-<xml name="manutest_SpectraSTSearchAdapter">\n-<test expect_num_outputs="2">\n- <conditional name="adv_opts_cond">\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="use_isotopically_averaged_mass" value="false"/>\n- <param name="use_all_charge_states" value="false"/>\n- <param name="force" value="false"/>\n- <param name="test" value="true"/>\n- </conditional>\n- <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/>\n- <param name="output_files_type" value="pep.xml"/>\n- <output_collection name="output_files" count="1"/>\n- <param name="library_file" value="testLib.splib" ftype="splib"/>\n- <param name="sequence_database_type" value="AA"/>\n- <param name="precursor_mz_tolerance" value="3.0"/>\n- <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>\n- <output name="ctd_out" ftype="xml">\n- <assert_contents>\n- <is_valid_xml/>\n- </assert_contents>\n- </output>\n- </test><test expect_num_outputs="2">\n- <conditional name="adv_opts_cond">\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="use_isotopically_averaged_mass" value="false"/>\n- <param name="use_all_charge_states" value="false"/>\n- <param name="force" value="false"/>\n- <param name="test" value="true"/>\n- </conditional>\n- <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/>\n- <param name="output_files_type" value="tsv"/>\n- <output_collection name="output_files" count="1"/>\n- <param name="library_file" value="testLib.splib" ftype="splib"/>\n- <param name="sequence_database_type" value="AA"/>\n- <param name="precursor_mz_tolerance" value="3.0"/>\n- <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>\n- <output name="ctd_out" ftype="xml">\n- <assert_contents>\n- <is_valid_xml/>\n- </assert_contents>\n- </output>\n- </test></xml>\n' |
| b |
| diff -r 047020d9012f -r 63fea23042c4 macros_test.xml --- a/macros_test.xml Sat Jan 30 11:38:47 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,553 +0,0 @@\n-<?xml version=\'1.0\' encoding=\'UTF-8\'?>\n-<macros>\n- \n-<!-- a copy of a FileConverter test without the advanced options used\n- in order to check if this works (all other tests enable advanced) -->\n-<xml name="manutest_FileConverter">\n-<test expect_num_outputs="1">\n- <param name="in" value="FileConverter_1_input.mzData"/>\n- <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>\n- <param name="out_type" value="mzML"/>\n-</test>\n-</xml>\n-<!-- tests contributed by the galaxyproteomics community -->\n-<xml name="manutest_ClusterMassTracesByPrecursor">\n- <test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML -->\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="adv_opts_cond|test" value="true"/>\n- <param name="in_ms1" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>\n- <param name="in_swath" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>\n- <output name="out" ftype="mzml" value="ClusterMassTracesByPrecursor.mzml"/>\n- </test>\n-</xml>\n-<xml name="manutest_ClusterMassTraces"> \n- <test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML -->\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="adv_opts_cond|test" value="true"/>\n- <param name="in" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>\n- <output name="out" ftype="mzml" value="ClusterMassTraces.mzml"/>\n- </test>\n-</xml>\n-<xml name="manutest_CVInspector">\n- <!-- test with https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo listed here https://www.psidev.info/groups/controlled-vocabularies, mapping file from share/OpenMS/MAPPING/ms-mapping.xml, see currently not working, see: https://github.com/OpenMS/OpenMS/pull/4425 -->\n- <test expect_num_outputs="1">\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="adv_opts_cond|test" value="true"/>\n- <param name="cv_files" ftype="obo" value="CHEMISTRY/XLMOD.obo"/>\n- <param name="cv_names" value="XLMOD"/>\n- <param name="mapping_file" value="MAPPING/ms-mapping.xml"/>\n- <param name="OPTIONAL_OUTPUTS" value="html_FLAG"/>\n- <output name="html" ftype="html" value="CVInspector.html"/>\n- </test>\n-</xml>\n-<xml name="manutest_DeMeanderize">\n- <test expect_num_outputs="1"><!-- test with the output of a MSsimulator output generated by a test below -->\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="adv_opts_cond|test" value="true"/>\n- <param name="in" ftype="mzml" value="MSsimulator_MALDI.mzml"/>\n-\t<output name="out" ftype="mzml" value="DeMeanderize.mzml"/>\n- </test>\n-</xml>\n-<xml name="manutest_Digestor">\n- <test expect_num_outputs="1"><!-- just using some random fasta, in contrast to DigestorMotif idXML/fasta output possible, testing for the non-default fasta option -->\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="adv_opts_cond|test" value="true"/>\n- <param name="in" ftype="fasta" value="random.fa"/>\n- <output name="out" ftype="fasta" value="Digestor.fasta"/>\n- <param name="out_type" value="fasta"/>\n- </test>\n-</xml>\n-<xml name="manutest_EICExtractor">\n- <test expect_num_outputs="1"><!-- just using some random test data -->\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="adv_opts_cond|test" value="true"/>\n- <param name="in" value="spectra.mzML"/>\n- <param name="pos" ftype="edta" value="FileConverter_10_input.edta"/>\n- <output name="out" ftype="csv" value="EICExtractor.csv" lines_diff="2"/>\n- </test>\n-</xml>\n-<xml name="manutest_ERPairFinder">\n- <!-- TODO -->\n-</xml>\n-<xml name="manutest_FeatureFinderIsotopeWavelet">\n- <test expect_num_outputs="1"><!--just use the input of another FeatureFinder -->\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="adv_opts_cond|test" value="true"/>\n- <param name="in" value="FeatureFin'..b'atureFinderMetabo"/><xml name="manutest_CruxAdapter"/><xml name="manutest_OpenSwathConfidenceScoring"/><xml name="manutest_PrecursorIonSelector"/><xml name="manutest_ConsensusMapNormalizer"/><xml name="manutest_RTPredict"/><xml name="manutest_PercolatorAdapter"/><xml name="manutest_ProteinInference"/><xml name="manutest_OpenSwathDecoyGenerator"/><xml name="manutest_TextExporter"/><xml name="manutest_FeatureFinderCentroided"/><xml name="manutest_DecoyDatabase"/><xml name="manutest_SpectraFilterWindowMower"/><xml name="manutest_NoiseFilterGaussian"/><xml name="manutest_MaRaClusterAdapter"/><xml name="manutest_ConsensusID"/><xml name="manutest_FileFilter"/><xml name="manutest_InclusionExclusionListCreator"/><xml name="manutest_FeatureLinkerUnlabeledKD"/><xml name="manutest_NovorAdapter"/><xml name="manutest_OpenPepXL"/><xml name="manutest_SeedListGenerator"/><xml name="manutest_FalseDiscoveryRate"/><xml name="manutest_OpenPepXLLF"/><xml name="manutest_SpecLibSearcher"/><xml name="manutest_IDConflictResolver"/><xml name="manutest_MRMMapper"/><xml name="manutest_OMSSAAdapter"/><xml name="manutest_ExternalCalibration"/><xml name="manutest_PeakPickerHiRes"/><xml name="manutest_MascotAdapter"/><xml name="manutest_FeatureFinderMultiplex"/><xml name="manutest_MetaProSIP"/><xml name="manutest_FuzzyDiff"/><xml name="manutest_TargetedFileConverter"/><xml name="manutest_MapAlignerIdentification"/><xml name="manutest_IDRTCalibration"/><xml name="manutest_MRMTransitionGroupPicker"/><xml name="manutest_RTModel"/><xml name="manutest_OpenSwathAssayGenerator"/><xml name="manutest_IDSplitter"/><xml name="manutest_OpenSwathMzMLFileCacher"/><xml name="manutest_HighResPrecursorMassCorrector"/><xml name="manutest_OpenSwathChromatogramExtractor"/><xml name="manutest_OpenSwathAnalyzer"/><xml name="manutest_FeatureLinkerUnlabeled"/><xml name="manutest_CompNovoCID"/><xml name="manutest_DTAExtractor"/><xml name="manutest_FileInfo"/><xml name="manutest_MapAlignerSpectrum"/><xml name="manutest_IsobaricAnalyzer"/><xml name="manutest_LowMemPeakPickerHiRes"/><xml name="manutest_MyriMatchAdapter"/><xml name="manutest_InternalCalibration"/><xml name="manutest_TOFCalibration"/><xml name="manutest_MSGFPlusAdapter"/><xml name="manutest_PTModel"/><xml name="manutest_InspectAdapter"/><xml name="manutest_SpectraFilterSqrtMower"/><xml name="manutest_SimpleSearchEngine"/><xml name="manutest_PeakPickerWavelet"/><xml name="manutest_MapNormalizer"/><xml name="manutest_IDScoreSwitcher"/><xml name="manutest_FeatureLinkerLabeled"/><xml name="manutest_MapRTTransformer"/><xml name="manutest_RNPxlSearch"/><xml name="manutest_PrecursorMassCorrector"/><xml name="manutest_MapAlignerPoseClustering"/><xml name="manutest_MzTabExporter"/><xml name="manutest_BaselineFilter"/><xml name="manutest_FeatureFinderMRM"/><xml name="manutest_MascotAdapterOnline"/><xml name="manutest_DatabaseFilter"/><xml name="manutest_ProteinResolver"/><xml name="manutest_OpenSwathFeatureXMLToTSV"/><xml name="manutest_FidoAdapter"/><xml name="manutest_AccurateMassSearch"/><xml name="manutest_CompNovo"/><xml name="manutest_LowMemPeakPickerHiResRandomAccess"/><xml name="manutest_OpenSwathRTNormalizer"/><xml name="manutest_PeptideIndexer"/><xml name="manutest_CometAdapter"/><xml name="manutest_NoiseFilterSGolay"/><xml name="manutest_MSFraggerAdapter"/><xml name="manutest_SpectraSTSearchAdapter"/><xml name="manutest_SequestAdapter"/><xml name="manutest_FeatureFinder"/><xml name="manutest_LuciphorAdapter"/><xml name="manutest_GNPSExport"/><xml name="manutest_Epifany"/><xml name="manutest_NucleicAcidSearchEngine"/><xml name="manutest_QualityControl"/><xml name="manutest_FeatureFinderMetaboIdent"/><xml name="manutest_RNAMassCalculator"/><xml name="manutest_MapAlignerTreeGuided"/><xml name="manutest_IDMassAccuracy"/><xml name="manutest_ProteomicsLFQ"/><xml name="manutest_IDDecoyProbability"/><xml name="manutest_DigestorMotif"/><xml name="manutest_DatabaseSuitability"/><xml name="manutest_StaticModification"/></macros>\n' |
| b |
| diff -r 047020d9012f -r 63fea23042c4 readme.md --- a/readme.md Sat Jan 30 11:38:47 2021 +0000 +++ b/readme.md Thu Dec 01 19:01:06 2022 +0000 |
| b |
| @@ -74,10 +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 047020d9012f -r 63fea23042c4 test-data.sh --- a/test-data.sh Sat Jan 30 11:38:47 2021 +0000 +++ b/test-data.sh Thu Dec 01 19:01:06 2022 +0000 |
| [ |
| b'@@ -1,22 +1,25 @@\n #!/usr/bin/env bash\n \n-VERSION=2.6\n-FILETYPES="filetypes.txt"\n-CONDAPKG="https://anaconda.org/bioconda/openms/2.6.0/download/linux-64/openms-2.6.0-h4afb90d_0.tar.bz2"\n+VERSION=2.8\n+FILETYPES="aux/filetypes.txt"\n+CONDAPKG="https://anaconda.org/bioconda/openms/2.8.0/download/linux-64/openms-2.8.0-h7ca0330_0.tar.bz2"\n \n # import the magic\n . ./generate-foo.sh\n \n # install conda\n if [ -z "$tmp" ]; then\n-\ttmp=$(mktemp -d)\n-\tcreated="yes"\n+ tmp=$(mktemp -d)\n+ created="yes"\n fi\n \n export OPENMSGIT="$tmp/OpenMS$VERSION.0-git"\n export OPENMSPKG="$tmp/OpenMS$VERSION-pkg/"\n-export OPENMSENV="$tmp/OpenMS$VERSION-env"\n-export CTDCONVERTER="$tmp/CTDConverter"\n+export OPENMSENV="OpenMS$VERSION-env"\n+\n+if [ -z "$CTDCONVERTER" ]; then\n+ export CTDCONVERTER="$tmp/CTDConverter"\n+fi\n \n if [[ -z "$1" ]]; then\n \tautotests="/dev/null"\n@@ -25,11 +28,11 @@\n fi\n \n if type conda > /dev/null; then \n-\ttrue\n+ true\n else\n-\twget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh\n-\tbash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda"\n-\tsource "$tmp/miniconda/bin/activate"\n+ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh\n+ bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda"\n+ source "$tmp/miniconda/bin/activate"\n fi\n eval "$(conda shell.bash hook)"\n \n@@ -42,24 +45,27 @@\n \n echo "Clone OpenMS $VERSION sources"\n if [[ ! -d $OPENMSGIT ]]; then\n-\tgit clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT\n-\tcd $OPENMSGIT\n-\tgit submodule init\n-\tgit submodule update\n-\tcd -\n+ # TODO >2.8 reenable original release branch .. also in else branch\n+ # the plus branch contains commits from https://github.com/OpenMS/OpenMS/pull/5920 and https://github.com/OpenMS/OpenMS/pull/5917\n+ # git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT\n+ git clone -b release/$VERSION.0-plus https://github.com/bernt-matthias/OpenMS.git $OPENMSGIT\n+ cd $OPENMSGIT\n+ git submodule init\n+ git submodule update\n+ cd -\n else\n-\tcd $OPENMSGIT\n-\tgit pull origin release/$VERSION.0\n-\tcd -\n+ cd $OPENMSGIT\n+ git pull origin release/$VERSION.0-plus\n+ cd -\n fi\n \n echo "Create OpenMS $VERSION conda env"\n # TODO currently add lxml (needed by CTDConverter)\n # TODO for some reason a to recent openjdk is used\n if conda env list | grep "$OPENMSENV"; then\n-\ttrue\n+ true\n else\n-\tconda 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\n+ conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -n $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION omssa=2.1.9 ctdopts=1.5 lxml\n # chmod -R u-w $OPENMSENV \n fi\n ###############################################################################\n@@ -69,10 +75,10 @@\n echo "Download OpenMS $VERSION package $CONDAPKG"\n \n if [[ ! -d $OPENMSPKG ]]; then\n-\tmkdir $OPENMSPKG\n-\twget -q -P $OPENMSPKG/ "$CONDAPKG"\n-\ttar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C $OPENMSPKG/\n-\trm $OPENMSPKG/"$(basename $CONDAPKG)"\n+ mkdir $OPENMSPKG\n+ wget -q -P $OPENMSPKG/ "$CONDAPKG"\n+ tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C $OPENMSPKG/\n+ rm $OPENMSPKG/"$(basename $CONDAPKG)"\n fi\n \n ###############################################################################\n@@ -81,40 +87,46 @@\n ###############################################################################\n echo "Clone CTDConverter"\n if [[ ! -d $CTDCONVERTER ]]; then\n-\t#git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter\n-\tgit clone -b topic/cdata https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER\n+ #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter\n+ git clone -b topic/fix-selects2 https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER\n else\n-\tcd $CTDCONVERTER\n-\tgi'..b'*/\\([^/]\\+\\).xml$@\\1@\' | tr \'\\n\' \'|\' | sed \'s/|$//\')\n+## else\n+## REX=".*"\n+## fi\n+## echo REX $REX\n+## cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh\n+## rm tmp_test_data.sh\n \n echo "Execute test shell script"\n chmod u+x prepare_test_data.sh\n@@ -204,14 +212,13 @@\n cd - || exit\n \n \n-###############################################################################\n-## create/update test data for the manually generated tests\n-## - run convert once with the manual tests only and \n-## - update test-data (needs to run 2x)\n-###############################################################################\n+# ###############################################################################\n+# ## create/update test data for the manually generated tests\n+# ## - run convert once with the manual tests only and \n+# ## - update test-data (needs to run 2x)\n+# ###############################################################################\n echo "Execute test shell script for manually curated tests"\n chmod u+x prepare_test_data_manual.sh\n-\n cd ./test-data || exit\n ../prepare_test_data_manual.sh\n cd - || exit\n@@ -220,22 +227,28 @@\n ###############################################################################\n ## auto generate tests\n ###############################################################################\n+\n echo "Write test macros to $autotests"\n echo "<macros>" > "$autotests"\n-for i in $(ls *xml |grep -v macros)\n+\n+for i in $(ls ctd/*ctd)\n do\n-\tb=$(basename "$i" .xml)\n-\tget_tests2 "$b" >> "$autotests"\n+ b=$(basename "$i" .ctd)\n+ get_tests2 "$b" >> "$autotests"\n done\n echo "</macros>" >> "$autotests"\n \n-echo "Create test data links"\n-link_tmp_files\n+# echo "Create test data links"\n+# Breaks DecoyDatabase\n+# link_tmp_files\n \n # tests for tools using output_prefix parameters can not be auto generated\n # hence we output the tests for manual curation in macros_test.xml\n # and remove them from the autotests\n-# -> OpenSwathFileSplitter IDRipper MzMLSplitter\n+# -> OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator\n+# TODO reevaluate in >2.8 \n+# - https://github.com/OpenMS/OpenMS/pull/5873\n+# - https://github.com/OpenMS/OpenMS/pull/5912\n #\n # Furthermore we remove tests for tools without binaries in conda\n # -> MSFragger MaRaClusterAdapter NovorAdapter \n@@ -243,23 +256,23 @@\n # not able to specify composite test data \n # -> SpectraSTSearchAdapter \n if [[ ! -z "$1" ]]; then\n-\techo "" > macros_discarded_auto.xml\n-\tfor i in OpenSwathFileSplitter IDRipper MzMLSplitter MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter\n-\tdo\n-\t\techo "<xml name=\\"manutest_$i\\">" >> macros_discarded_auto.xml\n-\t\txmlstarlet sel -t -c "/macros/xml[@name=\'autotest_$i\']/test" macros_autotest.xml >> macros_discarded_auto.xml\n-\t\techo "</xml>" >> macros_discarded_auto.xml\n-\t\txmlstarlet ed -d "/macros/xml[@name=\'autotest_$i\']/test" macros_autotest.xml > tmp\n-\t\tmv tmp macros_autotest.xml\n-\tdone\n-\t>&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml"\n+ echo "" > macros_discarded_auto.xml\n+ for i in OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter\n+ do\n+ echo "<xml name=\\"manutest_$i\\">" >> macros_discarded_auto.xml\n+ xmlstarlet sel -t -c "/macros/xml[@name=\'autotest_$i\']/test" macros_autotest.xml >> macros_discarded_auto.xml\n+ echo "</xml>" >> macros_discarded_auto.xml\n+ xmlstarlet ed -d "/macros/xml[@name=\'autotest_$i\']/test" macros_autotest.xml > tmp\n+ mv tmp macros_autotest.xml\n+ done\n+ >&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml"\n fi\n conda deactivate\n \n ## remove broken symlinks in test-data\n find test-data/ -xtype l -delete\n \n-# if [ ! -z "$created" ]; then\n-# \techo "Removing temporary directory"\n-# \trm -rf "$tmp"\n-# fi\n+if [ ! -z "$created" ]; then\n+ echo "Removing temporary directory"\n+ rm -rf "$tmp"\n+fi\n' |