| Previous changeset 6:eb22f145fae1 (2019-05-17) Next changeset 8:aa62f8f48dd4 (2020-09-24) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" |
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modified:
TargetedFileConverter.xml filetypes.txt macros.xml readme.md tools_blacklist.txt |
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added:
OMSSAAdapter.patch PepNovoAdapter.patch fill_ctd.py fill_ctd_clargs.py generate-foo.sh generate.sh hardcoded_params.json macros_autotest.xml macros_discarded_auto.xml macros_test.xml prepare_test_data.sh prepare_test_data_manual.sh test-data.sh tool-data/pepnovo_models.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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removed:
tool.conf |
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| diff -r eb22f145fae1 -r 51b9c2d5b4c3 OMSSAAdapter.patch --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OMSSAAdapter.patch Wed Sep 09 12:55:31 2020 +0000 |
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| @@ -0,0 +1,10 @@ +--- 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 eb22f145fae1 -r 51b9c2d5b4c3 PepNovoAdapter.patch --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PepNovoAdapter.patch Wed Sep 09 12:55:31 2020 +0000 |
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| @@ -0,0 +1,35 @@ +--- 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 eb22f145fae1 -r 51b9c2d5b4c3 TargetedFileConverter.xml --- a/TargetedFileConverter.xml Fri May 17 10:26:11 2019 -0400 +++ b/TargetedFileConverter.xml Wed Sep 09 12:55:31 2020 +0000 |
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| b'@@ -1,78 +1,93 @@\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: [Targeted Experiments]-->\n-<tool id="TargetedFileConverter" name="TargetedFileConverter" version="2.3.0">\n+<tool id="TargetedFileConverter" name="TargetedFileConverter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">\n <description>Converts different transition files for targeted proteomics / metabolomics analysis.</description>\n <macros>\n <token name="@EXECUTABLE@">TargetedFileConverter</token>\n <import>macros.xml</import>\n+ <import>macros_autotest.xml</import>\n+ <import>macros_test.xml</import>\n </macros>\n- <expand macro="references"/>\n+ <expand macro="requirements"/>\n <expand macro="stdio"/>\n- <expand macro="requirements"/>\n- <command detect_errors="aggressive"><![CDATA[TargetedFileConverter\n+ <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@\n+@EXT_FOO@\n+#import re\n+\n+## Preprocessing\n+mkdir in &&\n+ln -s \'$in\' \'in/${re.sub("[^\\w\\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)\' &&\n+mkdir out &&\n+\n+## Main program call\n \n-#if $param_in:\n- -in $param_in\n-#end if\n-#if $param_out:\n- -out $param_out\n-#end if\n-#if $param_out_type:\n- -out_type\n- #if " " in str($param_out_type):\n- "$param_out_type"\n- #else\n- $param_out_type\n- #end if\n-#end if\n-#if $adv_opts.adv_opts_selector==\'advanced\':\n- #if $adv_opts.param_legacy_traml_id:\n- -legacy_traml_id\n-#end if\n- #if $adv_opts.param_force:\n- -force\n-#end if\n- #if $adv_opts.param_algorithm_retentionTimeInterpretation:\n- -algorithm:retentionTimeInterpretation\n- #if " " in str($adv_opts.param_algorithm_retentionTimeInterpretation):\n- "$adv_opts.param_algorithm_retentionTimeInterpretation"\n- #else\n- $adv_opts.param_algorithm_retentionTimeInterpretation\n- #end if\n-#end if\n- #if $adv_opts.param_algorithm_override_group_label_check:\n- -algorithm:override_group_label_check\n-#end if\n- #if $adv_opts.param_algorithm_force_invalid_mods:\n- -algorithm:force_invalid_mods\n-#end if\n-#end if\n-]]></command>\n+set -o pipefail &&\n+@EXECUTABLE@ -write_ctd ./ &&\n+python3 \'$__tool_directory__/fill_ctd.py\' \'@EXECUTABLE@.ctd\' \'$args_json\' \'$hardcoded_json\' &&\n+@EXECUTABLE@ -ini @EXECUTABLE@.ctd\n+-in\n+\'in/${re.sub("[^\\w\\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)\'\n+-out\n+\'out/output.${out_type}\'\n+\n+## Postprocessing\n+&& mv \'out/output.${out_type}\' \'$out\'\n+#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS\n+ && mv \'@EXECUTABLE@.ctd\' \'$ctd_out\'\n+#end if]]></command>\n+ <configfiles>\n+ <inputs name="args_json" data_style="paths"/>\n+ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>\n+ </configfiles>\n <inputs>\n- <param name="param_in" type="data" format="tabular,mrm,pqp,traml" optional="False" label="Input file to convert" help="(-in) <br> See http://www.openms.de/current_doxygen/html/UTILS_TargetedFileConverter.html for format of OpenSWATH transition TSV file or SpectraST MRM file"/>\n- <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type -- default: determined from file extension or content <br>Note: that not all conversion paths work or make sense" help="(-out_type) ">\n- <option value="tsv">tsv</option>\n+ <param name="in" argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file to convert" help="See http://www.openms.de/current_doxygen/html/UTILS_TargetedFileConverter.html for format of OpenSWATH transition TSV file or SpectraST MRM file select mrm,pqp,tabular,traml data sets(s)"/>\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="Note: that not '..b'ime (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="">\n <option value="iRT" selected="true">iRT</option>\n <option value="seconds">seconds</option>\n <option value="minutes">minutes</option>\n+ <expand macro="list_string_san"/>\n </param>\n- <param name="param_algorithm_override_group_label_check" display="radio" type="boolean" truevalue="-algorithm:override_group_label_check" falsevalue="" checked="false" optional="True" label="Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group)" help="(-override_group_label_check) Only turn this off if you know what you are doing"/>\n- <param name="param_algorithm_force_invalid_mods" display="radio" type="boolean" truevalue="-algorithm:force_invalid_mods" falsevalue="" checked="false" optional="True" label="Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)" help="(-force_invalid_mods) "/>\n+ <param name="override_group_label_check" argument="-algorithm:override_group_label_check" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group)" help="Only turn this off if you know what you are doing"/>\n+ <param name="force_invalid_mods" argument="-algorithm:force_invalid_mods" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)" help=""/>\n+ </section>\n+ <expand macro="adv_opts_macro">\n+ <param name="legacy_traml_id" argument="-legacy_traml_id" type="boolean" truevalue="true" falsevalue="false" checked="false" label="PQP to TraML: Should legacy TraML IDs be used?" help=""/>\n+ <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite 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>\n </expand>\n+ <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">\n+ <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>\n+ </param>\n </inputs>\n <outputs>\n- <data name="param_out" metadata_source="param_in" format="input"/>\n+ <data name="out" label="${tool.name} on ${on_string}: out">\n+ <change_format>\n+ <when input="out_type" value="TraML" format="traml"/>\n+ <when input="out_type" value="pqp" format="pqp"/>\n+ <when input="out_type" value="tsv" format="tabular"/>\n+ </change_format>\n+ </data>\n+ <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">\n+ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>\n+ </data>\n </outputs>\n- <help>Converts different transition files for targeted proteomics / metabolomics analysis.\n+ <tests>\n+ <expand macro="autotest_TargetedFileConverter"/>\n+ <expand macro="manutest_TargetedFileConverter"/>\n+ </tests>\n+ <help><![CDATA[Converts different transition files for targeted proteomics / metabolomics analysis.\n \n \n-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_TargetedFileConverter.html</help>\n+For more information, visit http://www.openms.de/documentation/UTILS_TargetedFileConverter.html]]></help>\n+ <expand macro="references"/>\n </tool>\n' |
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| diff -r eb22f145fae1 -r 51b9c2d5b4c3 filetypes.txt --- a/filetypes.txt Fri May 17 10:26:11 2019 -0400 +++ b/filetypes.txt Wed Sep 09 12:55:31 2020 +0000 |
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| @@ -1,29 +1,85 @@ -# CTD type # Galaxy type # Long Galaxy data type # Mimetype -csv tabular galaxy.datatypes.tabular:Tabular -fasta fasta galaxy.datatypes.sequence:Fasta -FASTA fasta galaxy.datatypes.sequence:Fasta -ini txt galaxy.datatypes.data:Text -txt txt galaxy.datatypes.data:Text -options txt galaxy.datatypes.data:Text -grid grid galaxy.datatypes.data:Grid -html html galaxy.datatypes.text:Html text/html -HTML html galaxy.datatypes.text:Html text/html -TraML traml galaxy.datatypes.proteomics:TraML application/xml -traML traml galaxy.datatypes.proteomics:TraML application/xml -XML xml galaxy.datatypes.xml:GenericXml application/xml -consensusXML consensusxml galaxy.datatypes.proteomics:ConsensusXML application/xml -edta tabular galaxy.datatypes.tabular:Tabular -featureXML featurexml galaxy.datatypes.proteomics:FeatureXML application/xml -idXML idxml galaxy.datatypes.proteomics:IdXML application/xml -mzML mzml galaxy.datatypes.proteomics:MzML application/xml -mzXML mzxml galaxy.datatypes.proteomics:MzXML application/xml -pepXML pepxml galaxy.datatypes.proteomics:PepXml application/xml -qcML qcml galaxy.datatypes.xml:GenericXml application/xml -trafoXML trafoxml galaxy.datatypes.xml:GenericXml application/xml -tsv tabular galaxy.datatypes.tabular:Tabular -xsd txt galaxy.datatypes.data:Text -mzq mzq galaxy.datatypes.proteomics:MzQuantML application/xml -msp msp galaxy.datatypes.proteomics:Msp -mzid mzid galaxy.datatypes.proteomics:MzIdentML application/xml -png png galaxy.datatypes.images:Png image/png -mgf mgf galaxy.datatypes.proteomics:Mgf +# 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 +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 eb22f145fae1 -r 51b9c2d5b4c3 fill_ctd.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fill_ctd.py Wed Sep 09 12:55:31 2020 +0000 |
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| @@ -0,0 +1,190 @@ +import collections +import json +import operator +import os +import re +import subprocess +import sys +from functools import reduce # forward compatibility for Python 3 + +from CTDopts.CTDopts import ( + _Choices, + _InFile, + _Null, + _NumericRange, + CTDModel +) + + +def getFromDict(dataDict, mapList): + return reduce(operator.getitem, mapList, dataDict) + + +def setInDict(dataDict, mapList, value): + getFromDict(dataDict, mapList[:-1])[mapList[-1]] = value + + +def mergeDicts(d, e): + """ + insert values from the dict e into dict d + no values of d are overwritten + """ + 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): + d[k] = e[k] + else: + sys.stderr.write("fill_ctd.py: could not merge key %s for %s in %s" % (k, d, e)) + sys.exit(1) + + +def _json_object_hook_noenvlookup(d): + return _json_object_hook(d, envlookup=False) + + +def _json_object_hook(d, envlookup=True): + """ + wee helper to transform the json written by galaxy + while loading + - True/False (bool objects) -> "true"/"false" (lowercase string) + - data inputs with multiple and optional true give [None] if no file is given -> [] + - None -> "" (empty string) + - replace bash expressions (if envlookup is True): + - environment variables (need to consist capital letters and _) by their value + - expressions + """ + for k in d.keys(): + # if type(d[k]) is bool: + # d[k] = str(d[k]).lower() + # else + if type(d[k]) is list and len(d[k]) == 1 and d[k][0] is None: + d[k] = [] + elif d[k] is None: + d[k] = "" + elif envlookup and type(d[k]) is str and d[k].startswith("$"): + m = re.fullmatch(r"\$([A-Z_]+)", d[k]) + if m: + d[k] = os.environ.get(m.group(1), "") + continue + m = re.fullmatch(r"\$(\{[A-Z_]+):-(.*)\}", d[k]) + if m: + d[k] = os.environ.get(m.group(1), m.group(2)) + continue + + try: + p = subprocess.run("echo %s" % d[k], shell=True, check=True, stdout=subprocess.PIPE, encoding="utf8") + d[k] = p.stdout.strip() + except subprocess.CalledProcessError: + sys.stderr.write("fill_ctd error: Could not evaluate %s" % d[k]) + continue + return d + + +def qstring2list(qs): + """ + transform a space separated string that is quoted by " into a list + """ + lst = list() + qs = qs.split(" ") + quoted = False + for p in qs: + if p == "": + continue + if p.startswith('"') and p.endswith('"'): + lst.append(p[1:-1]) + elif p.startswith('"'): + quoted = True + lst.append(p[1:] + " ") + elif p.endswith('"'): + quoted = False + lst[-1] += p[:-1] + else: + if quoted: + lst[-1] += p + " " + else: + lst.append(p) + return lst + + +def fix_underscores(args): + if type(args) is dict: + for k in list(args.keys()): + v = args[k] + if type(v) is dict: + fix_underscores(args[k]) + if k.startswith("_"): + args[k[1:]] = v + del args[k] + elif type(args) is list: + for i, v in enumerate(args): + if type(v) is dict: + fix_underscores(args[i]) + + +input_ctd = sys.argv[1] + +# load user specified parameters from json +with open(sys.argv[2]) as fh: + args = json.load(fh, object_hook=_json_object_hook_noenvlookup) + +# load hardcoded parameters from json +with open(sys.argv[3]) as fh: + hc_args = json.load(fh, object_hook=_json_object_hook) + +# 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"] + +# 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" +# therefore hardcoded params change the name of spectra:in to spectra:_in +# which is corrected here again +# TODO remove once PR is in and adapt profile accordingly +fix_underscores(args) + +model = CTDModel(from_file=input_ctd) + +# transform values from json that correspond to +# - old style booleans (string + restrictions) -> transformed to a str +# - unrestricted ITEMLIST which are represented as strings +# ("=quoted and space separated) in Galaxy -> transform to lists +# - optional data input parameters that have defaults and for which no +# value is given -> overwritte with the default +for p in model.get_parameters(): + + # check if the parameter is in the arguments from the galaxy tool + # (from the json file(s)), since advanced parameters are absent + # if the conditional is set to basic parameters + try: + getFromDict(args, p.get_lineage(name_only=True)) + except KeyError: + # few tools use dashes in parameters which are automatically replaced + # by underscores by Galaxy. in these cases the dictionary needs to be + # updated + # TODO might be removed later https://github.com/OpenMS/OpenMS/pull/4529 + try: + lineage = [_.replace("-", "_") for _ in p.get_lineage(name_only=True)] + val = getFromDict(args, lineage) + except KeyError: + continue + else: + setInDict(args, lineage, val) + + if p.type is str and type(p.restrictions) is _Choices and set(p.restrictions.choices) == set(["true", "false"]): + v = getFromDict(args, p.get_lineage(name_only=True)) + setInDict(args, p.get_lineage(name_only=True), str(v).lower()) + + elif p.is_list and (p.restrictions is None or type(p.restrictions) is _NumericRange): + v = getFromDict(args, p.get_lineage(name_only=True)) + if type(v) is str: + setInDict(args, p.get_lineage(name_only=True), qstring2list(v)) + elif p.type is _InFile and not (p.default is None or type(p.default) is _Null): + v = getFromDict(args, p.get_lineage(name_only=True)) + if v in [[], ""]: + setInDict(args, p.get_lineage(name_only=True), p.default) + +model.write_ctd(input_ctd, arg_dict=args) |
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| diff -r eb22f145fae1 -r 51b9c2d5b4c3 fill_ctd_clargs.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fill_ctd_clargs.py Wed Sep 09 12:55:31 2020 +0000 |
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| @@ -0,0 +1,40 @@ +#!/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 eb22f145fae1 -r 51b9c2d5b4c3 generate-foo.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate-foo.sh Wed Sep 09 12:55:31 2020 +0000 |
| [ |
| b'@@ -0,0 +1,217 @@\n+#!/usr/bin/env bash\n+\n+# parse test definitions from OpenMS sources for a tool with a given id\n+function get_tests2 {\n+\tid=$1\n+\t>&2 echo "generate tests for $id"\n+\techo \'<xml name="autotest_\'"$id"\'">\'\n+\n+\t# get the tests from the CMakeLists.txt\n+\t# 1st remove some tests\n+\t# - Filefilter with empty select_palarity value (empty is not in the list of allowed options)\n+\t# - MassTraceExtractor with outdated ini file leading to wrong parameters https://github.com/OpenMS/OpenMS/issues/4386\n+\t# - OpenSwathMzMLFileCacher with -convert_back argumen https://github.com/OpenMS/OpenMS/issues/4399\n+ # - IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differentlt\n+\t# - several tools with duplicated input (leads to conflict when linking)\n+\t# - TOFCalibration inputs we extension (also in prepare_test_data) https://github.com/OpenMS/OpenMS/pull/4525\n+\t# - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456)\n+\t# - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed)\n+\t# - some input files are originally in a subdir (degenerated cases/), but not in test-data\n+\t# - SeedListGenerator: https://github.com/OpenMS/OpenMS/issues/4404\n+\t# - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet)\n+\tCMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake |\n+\t\tsed \'s@${DATA_DIR_SHARE}/@@g\' |\n+\t\tgrep -v \'OpenSwathMzMLFileCacher .*-convert_back\' |\n+\t \tsed \'s/${TMP_RIP_PATH}/""/\' |\n+\t\tsed \'s@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @\' |\n+\t\tgrep -v "MaRaClusterAdapter.*-consensus_out"|\n+ \t\tgrep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " |\n+\t\tsed \'s@degenerate_cases/@@g\' |\n+\t\tgrep -v \'TOPP_SeedListGenerator_3"\' | \n+\t\tegrep -v \'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"\')\n+\n+\n+# \t\tgrep -v \'FileFilter.*-spectra:select_polarity ""\' |\n+# \t\tgrep -v \'MassTraceExtractor_2.ini \' |\n+# \t\tgrep -v "FileMerger_6_input2.mzML.*FileMerger_6_input2.mzML" |\n+# \t\tgrep -v "IDMerger_1_input1.idXML.*IDMerger_1_input1.idXML" |\n+# \t\tgrep -v "degenerated_empty.idXML.*degenerated_empty.idXML" |\n+# \t\tgrep -v "FeatureLinkerUnlabeledKD_1_output.consensusXML.*FeatureLinkerUnlabeledKD_1_output.consensusXML" |\n+# \t\tgrep -v "FeatureLinkerUnlabeledQT_1_output.consensusXML.*FeatureLinkerUnlabeledQT_1_output.consensusXML" |\n+\n+\t# 1st part is a dirty hack to join lines containing a single function call, e.g.\n+\t# addtest(....\n+\t# ....)\n+\techo "$CMAKE" | sed \'s/#.*//; s/^\\s*//; s/\\s*$//\' | grep -v "^#" | grep -v "^$" | awk \'{printf("%s@NEWLINE@", $0)}\' | sed \'s/)@NEWLINE@/)\\n/g\' | sed \'s/@NEWLINE@/ /g\' | \n+\t\tgrep -iE "add_test\\(\\"(TOPP|UTILS)_.*/$id " | egrep -v "_prepare\\"|_convert|WRITEINI|WRITECTD|INVALIDVALUE" | while read -r line\n+\tdo\n+\t\tline=$(echo "$line" | sed \'s/add_test("\\([^"]\\+\\)"/\\1/; s/)$//; s/\\${TOPP_BIN_PATH}\\///g;s/\\${DATA_DIR_TOPP}\\///g; s#THIRDPARTY/##g\')\n+\t\t# >&2 echo $line\n+\t\ttest_id=$(echo "$line" | cut -d" " -f 1)\n+\t\ttool_id=$(echo "$line" | cut -d" " -f 2)\n+\t\tif [[ $test_id =~ _out_?[0-9]? ]]; then\n+\t\t\t>&2 echo " skip $test_id $line"\n+\t\t\tcontinue\n+\t\tfi\n+\t\tif [[ ${id,,} != ${tool_id,,} ]]; then\n+\t\t\t>&2 echo " skip $test_id ($id != $tool_id) $line"\n+\t\t\tcontinue\n+\t\tfi\n+\n+\t\t#remove tests with set_tests_properties(....PROPERTIES WILL_FAIL 1)\n+\t\tif grep -lq "$test_id"\'\\".* PROPERTIES WILL_FAIL 1\' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then\n+\t\t\t>&2 echo " skip failing "$test_id\n+\t\t\tcontinue\n+\t\tfi\n+\t\ttes=" <test>\\n"\n+\t\tline=$(fix_tmp_files "$line")\n+\t\tline=$(unique_files "$line")\n+\t\t# >&2 echo $line\n+\t\t#if there is an ini file then we use this to generate the test\n+\t\t#otherwise the ctd file is used\n+\t\t#other command line parameters are inserted later into this xml\n+\t\tif grep -lq "\\'..b'f to the expected file.\n+#problem: the extension of the tmp files is unusable for test generation.\n+#unfortunately the extensions used in the DIFF lines are not always usable for the CLI\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+#\t>&2 echo "FIX $line"\n+\tret=""\n+\tfor a in $@; do\n+\t\tif [[ ! $a =~ .tmp$ ]]; then\n+\t\t\tret="$ret $a"\n+\t\t\tcontinue\n+\t\tfi\n+#\t\t>&2 echo " a "$a\n+\t\tg=$(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}.*\'"$a")\n+#\t\t>&2 echo " g "$g\n+\t\tin1=$(sed \'s/.*-in1 \\([^ ]\\+\\).*/\\1/\' <<<$g)\n+\t\t# >&2 echo " in1 "$in1\n+\t\tif [[ "$a" != "$in1" ]]; then\n+\t\t\tret="$ret $a"\n+\t\t\tcontinue\n+\t\tfi\n+\t\tin2=$(sed \'s/.*-in2 \\([^ ]\\+\\).*/\\1/\' <<<$g)\n+\t\tin2=$(basename $in2 | sed \'s/)$//\')\n+\t\t# >&2 echo " in2 "$in2\n+\t\tif [[ -f "test-data/$in2" ]]; then\n+\t\t\tln -fs "$in1" "test-data/$in2"\n+\t\t\tret="$ret $in2"\n+\t\telse\n+\t\t\tret="$ret $a"\n+\t\tfi\n+\tdone\n+#\t>&2 echo "--> $ret"\n+\techo "$ret"\n+}\n+\n+function link_tmp_files {\n+ # note this also considers commented lines (starting with a #)\n+ # because of tests where the diff command is commented and we\n+ # still want to use the extension of these files\n+ cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed \'s/^\\s*//; s/\\s*$//\' | grep -v "^$" | awk \'{printf("%s@NEWLINE@", $0)}\' | sed \'s/)@NEWLINE@/)\\n/g\' | sed \'s/@NEWLINE@/ /g\' | grep "\\${DIFF}" | while read -r line\n+ do\n+ in1=$(sed \'s/.*-in1 \\([^ ]\\+\\).*/\\1/\' <<<$line)\n+ in1=$(basename $in1 | sed \'s/)$//\')\n+ in2=$(sed \'s/.*-in2 \\([^ ]\\+\\).*/\\1/\' <<<$line)\n+ in2=$(basename $in2 | sed \'s/)$//\')\n+ if [[ "$in1" == "$in2" ]]; then\n+ >&2 echo "not linking equal $in1 $in2"\n+ continue\n+ fi\n+ ln -f -s $in1 test-data/$in2\n+ done\n+ for i in test-data/*.tmp\n+ 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+ done\n+}\n+\n+\n+\n+# parse data preparation calls from OpenMS sources for a tool with a given id\n+function prepare_test_data {\n+# \tid=$1\n+# | egrep -i "$id\\_.*[0-9]+(_prepare\\"|_convert)?"\n+\tcat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed \'s/#.*$//\'| sed \'s/^\\s*//; s/\\s*$//\' | grep -v "^$" | awk \'{printf("%s@NEWLINE@", $0)}\' | sed \'s/)@NEWLINE@/)\\n/g\' | sed \'s/@NEWLINE@/ /g\' | \n+\t\tsed \'s/degenerate_cases\\///\' | \n+\t\tegrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | \n+\t\tgrep add_test | \n+\t\tegrep "TOPP|UTILS" |\n+\t\tsed \'s@${DATA_DIR_SHARE}/@@g;\'|\n+\t\tsed \'s@${TMP_RIP_PATH}@dummy2.tmp@g\'|\n+\t\tsed \'s@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @\'| \n+\twhile read line\n+\tdo\n+\t\ttest_id=$(echo "$line" | sed \'s/add_test(//; s/"//g; s/)[^)]*$//; s/\\${TOPP_BIN_PATH}\\///g;s/\\${DATA_DIR_TOPP}\\///g; s#THIRDPARTY/##g\' | cut -d" " -f1)\n+\n+\t\tif grep -lq "$test_id"\'\\".* PROPERTIES WILL_FAIL 1\' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then\n+\t\t\t>&2 echo " skip failing "$test_id\n+\t\t\tcontinue\n+\t\tfi\n+\n+\t\tline=$(echo "$line" | sed \'s/add_test("//; s/)[^)]*$//; s/\\${TOPP_BIN_PATH}\\///g;s/\\${DATA_DIR_TOPP}\\///g; s#THIRDPARTY/##g\' | cut -d" " -f2-)\n+\t\t# line="$(fix_tmp_files $line)"\n+\t\techo "$line > $test_id.stdout 2> $test_id.stderr"\n+\t\techo "if [[ \\"\\$?\\" -ne \\"0\\" ]]; then >&2 echo \'$test_id failed\'; >&2 echo -e \\"stderr:\\n\\$(cat $test_id.stderr | sed \'s/^/ /\')\\"; echo -e \\"stdout:\\n\\$(cat $test_id.stdout)\\";fi"\t\n+ done\n+}\n' |
| b |
| diff -r eb22f145fae1 -r 51b9c2d5b4c3 generate.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate.sh Wed Sep 09 12:55:31 2020 +0000 |
| [ |
| @@ -0,0 +1,76 @@ +#!/usr/bin/env bash + +# VERSION=2.3 +# CONDAPKG=https://anaconda.org/bioconda/openms/2.3.0/download/linux-64/openms-2.3.0-py27h932d754_3.tar.bz2 +# VERSION=2.4 +# CONDAPKG=https://anaconda.org/bioconda/openms/2.4.0/download/linux-64/openms-2.4.0-py27h574aadf_1.tar.bz2 + +VERSION=2.5 +FILETYPES="filetypes.txt" +PROFILE="20.05" +## FILETYPES_RE=$(grep -v "^#" $FILETYPES | grep -v "^$" | cut -f 1 -d" " | tr '\n' '|' | sed 's/|$//'| sed 's/|/\\|/g') + +export tmp=$(mktemp -d) + +export CTDCONVERTER="$tmp/CTDConverter" + +export PYTHONPATH="$(pwd)/CTDopts/" +############################################################################### +## reset old data +############################################################################### +# 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 +############################################################################### +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$(cat convert.err)"; fi +conda deactivate + +patch PepNovoAdapter.xml < PepNovoAdapter.patch +patch OMSSAAdapter.xml < OMSSAAdapter.patch + +# #-b version log debug test in_type executable pepnovo_executable param_model_directory rt_concat_trafo_out param_id_pool + +# for i in A-E F-H I-L M-N O-P Q-Z +# do +# planemo t [$i]*xml --galaxy_branch release_20.05 --galaxy_python_version 3.7 --test_output $i.html --test_output_json $i.json & +# done |
| b |
| diff -r eb22f145fae1 -r 51b9c2d5b4c3 hardcoded_params.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hardcoded_params.json Wed Sep 09 12:55:31 2020 +0000 |
| [ |
| @@ -0,0 +1,247 @@ +{ + "#": "blacklist parameters", + + "version": [{"value": "@"}], + "debug": [{"value": "@"}], + "algorithm:debug": [{"value": "@"}], + "java_memory": [{"value": "@"}], + "java_permgen": [{"value": "@"}], + "#": "type of input is always determined from the file extension ", + "in_type": [{"value": "@"}], + + "#": "tool specific blacklist parameters", + + "convert_back": [{"value": "@", "tools": ["OpenSwathMzMLFileCacher"]}], + "NET_executable": [{ + "value": "@", + "tools": ["FileConverter"] + }], + + + "params_file": [{"value": "@", "tools": ["SpectraSTSearchAdapter"]}], + + "#": "TODO not usable in 2.5 https://github.com/OpenMS/OpenMS/issues/4456, corresponding test currently disabled", + "consensus_out": [{"value": "@", "tools": ["MaRaClusterAdapter"]}], + "#": "TODO would need treatment as prefix-output", + "output_directory": [{"value": "@", "tools": ["MaRaClusterAdapter"]}], + + "#": "hardcode parameter values", + + "comet_version": [{ + "value":"2016.01 rev. 3" + }], + "comet_executable": [{ + "value":"comet" + }], + "crux_executable": [{ + "value": "crux" + }], + "fido_executable": [{ + "value":"Fido" + }], + "fidocp_executable": [{ + "value":"FidoChooseParameters" + }], + "maracluster_executable": [{ + "value":"/home/berntm/projects/tools-galaxyp/tools/openms/OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster" + }], + "mascot_directory": [{ + "value":"TODO" + }], + "myrimatch_executable": [{ + "value":"myrimatch" + }], + "omssa_executable": [{ + "value":"$(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}" + }], + "#": "hardcode the outer loop threads for OpenSwathWorkflow", + "outer_loop_threads": [{ + "value": "1", + "tools": ["OpenSwathWorkflow"] + }], + "separator": [{ + "value": ",", + "tools": ["IDMassAccuracy"] + }], + "#": "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", + "#": "MascotAdapter: https://github.com/OpenMS/OpenMS/pull/4553", + "#": "Phosphoscoring: https://github.com/OpenMS/OpenMS/pull/4569", + "#": "MzMLSplitter output prefix https://github.com/OpenMS/OpenMS/issues/4404", + "#": "IDRipper: blacklist out (is doing the same as the output-prefix out-path)", + "out": [{ + "CTD:is_list": false, + "tools": ["SeedListGenerator"] + }, { + "CTD:required": true, + "tools": ["FileInfo", "MapStatistics", "SequenceCoverageCalculator"] + }, { + "CTD:restrictions": "idXML", + "tools": ["MascotAdapter"] + }, { + "CTD:restrictions": "idXML", + "tools": ["PhosphoScoring"] + }, { + "CTD:type": "output-prefix", + "CTD:required": "true", + "CTD:restrictions": "mzml", + "tools": ["MzMLSplitter"] + }, { + "value": "@", + "tools": ["IDRipper"] + }], + + "#": "https://github.com/OpenMS/OpenMS/pull/4552 .. if this is removed the test will need out_cm_FLAG", + "out_cm": [{ + "CTD:required": true, + "tools": ["MetaboliteAdductDecharger"] + }], + + + "#": "https://github.com/OpenMS/OpenMS/pull/4451", + "out_xquestxml": [{ + "CTD:restrictions": "xquest.xml", + "tools": ["OpenPepXL", "OpenPepXLLF"] + }], + "out_xquest_specxml": [{ + "CTD:restrictions": "spec.xml", + "tools": ["OpenPepXL", "OpenPepXLLF"] + }], + + "#": "Try to remove xml data type whereever possible", + "#": "XTandem Adapter output is called .xml in OMS -> use Galaxy's bioml", + "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", + "#": "SpectraSTSearchAdapter does not need xml .. redundant with pep.xml TODO check if list is up to date with each new release", + "#": "SeedListGenerator https://github.com/OpenMS/OpenMS/issues/4404 .. see also out parameter", + "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": "txt,tsv,pep.xml,pepXML,html", + "tools": ["SpectraSTSearchAdapter"] + }, { + "CTD:restrictions": "mzML,idXML,featureXML", + "tools": ["SeedListGenerator"] + }], + + "#": "parameter is a flag but restrictions in wrong order: TODO https://github.com/OpenMS/OpenMS/pull/4455", + "# masstrace_snr_filtering": [{ + "CTD:restrictions": "true,false", + "tools": ["MassTraceExtractor"] + }], + + "#": "IDMapper has in and spectra:in params, in is used in out as format_source", + "#": "which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493", + "spectra:in": [{ + "CTD:name": "_in", + "tools": ["IDMapper"] + }], + + "#": "output-prefix", + "out_path": [{ + "CTD:type": "output-prefix", + "CTD:required": "true", + "CTD:restrictions": "idXML", + "tools": ["IDRipper"] + }], + "outputDirectory": [{ + "CTD:type": "output-prefix", + "CTD:required": "true", + "CTD:restrictions": "mzml", + "tools": ["OpenSwathFileSplitter"] + }] +} |
| b |
| diff -r eb22f145fae1 -r 51b9c2d5b4c3 macros.xml --- a/macros.xml Fri May 17 10:26:11 2019 -0400 +++ b/macros.xml Wed Sep 09 12:55:31 2020 +0000 |
| [ |
| @@ -1,11 +1,21 @@ <?xml version='1.0' encoding='UTF-8'?> +<!-- CTD2Galaxy depends on this file and on the stdio, advanced_options macros! + You can edit this file to add your own macros, if you so desire, or you can + add additional macro files using the m/macros parameter --> <macros> + <token name="@TOOL_VERSION@">2.5</token> + <token name="@GALAXY_VERSION@">0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="2.3">openms</requirement> - <requirement type="package" version="15.12.15.2">xtandem</requirement> - <requirement type="package" version="1.0">fido</requirement> - <requirement type="package" version="2017.07.21">msgf_plus</requirement> + <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> + <requirement type="package" version="8.0.192">openjdk</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>--> + <requirement type="package" version="1.4">ctdopts</requirement> <yield/> </requirements> </xml> @@ -21,8 +31,8 @@ <citation type="doi">doi:10.1186/1471-2105-9-163</citation> </citations> </xml> - <xml name="advanced_options"> - <conditional name="adv_opts"> + <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> @@ -33,4 +43,87 @@ </when> </conditional> </xml> -</macros> + + <!-- 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 ")">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator> + </xml> + <xml name="list_string_san"> + <sanitizer> + <valid initial="string.printable"> +<!-- <remove value="'"/>--> +<!-- <remove value="\"/>--><!-- otherwise the user could quote the final quote --> +<!-- <remove value="`"/>--> +<!-- <remove value="$"/>--> +<!-- <remove value="<"/>--> + <!--<remove value="&"/> removed for MascotAdapterOnline -Mascot_server:export_params which is a URL POST string which can contain & .. could be mapped to & but there is still a & --> + <!--<remove value=";"/>--> +<!-- <remove value="#"/>--> + </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]+)?)* *$</validator> + <yield/> + <sanitizer> + <valid initial="string.digits"> + <add value=" "/> + <add value="."/> + <add value="E"/> + <add value="e"/> + <add value="+"/> + <add value="-"/> + </valid> + </sanitizer> + </xml> + <xml name="list_integer_valsan"> + <validator type="regex" message="a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator> + <yield/> + <sanitizer> + <valid initial="string.digits"> + <add value=" "/> + <add value="+"/> + <add value="-"/> + </valid> + </sanitizer> + </xml> + + <!-- helper function to quote space separated strings --> + <token name="@QUOTE_FOO@"> +#def quote(s): + #set $s = [ _ for _ in $s.split(" ") if _ != "" ] + #set $q = False + #for $i, $p in enumerate($s): + #if $p == "": + #continue + #end if + #if $p.startswith('"'): + #set $q = True + #end if +## #if p.startswith('-'): +## #set p = "\\" + p +## #elif p.startswith('"-'): +## #set p = "\\" + p[1:] +## #end if + #if not $q: + #set $s[i] = '"%s"' % p + #end if + #if $p.endswith('"'): + #set $q = False + #end if + #end for + #return " ".join($s) +#end def + </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'} + #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'} + #return m[g] +#end def +]]></token></macros> |
| b |
| diff -r eb22f145fae1 -r 51b9c2d5b4c3 macros_autotest.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_autotest.xml Wed Sep 09 12:55:31 2020 +0000 |
| b |
| b'@@ -0,0 +1,26318 @@\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' <param name="minscore" value="0.0"/>\n+ <param name="binsize" value="0.1"/>\n+ <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_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_XMLValidator">\n+</xml>\n+ <xml name="autotest_XTandemAdapter">\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_1_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="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+ </xml>\n+<xml name="autotest_IDDecoyProbability"/><xml name="autotest_PTPredict"/><xml name="autotest_OpenSwathDIAPreScoring"/><xml name="autotest_Digestor"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_InspectAdapter"/><xml name="autotest_DigestorMotif"/><xml name="autotest_RTPredict"/><xml name="autotest_ProteomicsLFQ"/></macros>\n' |
| b |
| diff -r eb22f145fae1 -r 51b9c2d5b4c3 macros_discarded_auto.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_discarded_auto.xml Wed Sep 09 12:55:31 2020 +0000 |
| b |
| b'@@ -0,0 +1,378 @@\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="adv_opts_cond.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+ '..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 eb22f145fae1 -r 51b9c2d5b4c3 macros_test.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_test.xml Wed Sep 09 12:55:31 2020 +0000 |
| b |
| b'@@ -0,0 +1,549 @@\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'e="manutest_PTPredict"/><xml name="manutest_XTandemAdapter"/><xml name="manutest_FeatureFinderMetabo"/><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"/></macros>\n' |
| b |
| diff -r eb22f145fae1 -r 51b9c2d5b4c3 prepare_test_data.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/prepare_test_data.sh Wed Sep 09 12:55:31 2020 +0000 |
| [ |
| b'@@ -0,0 +1,1196 @@\n+export COMET_BINARY="comet"\n+export CRUX_BINARY="crux"\n+export FIDOCHOOSEPARAMS_BINARY="FidoChooseParameters"\n+export FIDO_BINARY="Fido"\n+export LUCIPHOR_BINARY="$(dirname $(realpath $(which luciphor2)))/luciphor2.jar"\n+export MARACLUSTER_BINARY="/tmp/openms-stuff//OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster"\n+export MSFRAGGER_BINARY="/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar"\n+export MSGFPLUS_BINARY="$(msgf_plus -get_jar_path)"\n+export MYRIMATCH_BINARY="myrimatch"\n+export NOVOR_BINARY="/home/berntm/Downloads/novor/lib/novor.jar"\n+export OMSSA_BINARY="$(dirname $(realpath $(which omssacl)))/omssacl"\n+export PERCOLATOR_BINARY="percolator"\n+export SIRIUS_BINARY="$(which sirius)"\n+export SPECTRAST_BINARY="spectrast"\n+export XTANDEM_BINARY="xtandem"\n+export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"\n+FuzzyDiff -test -ini FuzzyDiff.ini -in1 FuzzyDiff_3_in1.featureXML -in2 FuzzyDiff_3_in2.featureXML > UTILS_FuzzyDiff_3.stdout 2> UTILS_FuzzyDiff_3.stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'UTILS_FuzzyDiff_3 failed\'; >&2 echo -e "stderr:\\n$(cat UTILS_FuzzyDiff_3.stderr | sed \'s/^/ /\')"; echo -e "stdout:\\n$(cat UTILS_FuzzyDiff_3.stdout)";fi\n+IDMerger -test -in IDMerger_1_input1.idXML IDMerger_1_input2.idXML -out IDMerger_1_output.tmp -annotate_file_origin > TOPP_IDMerger_1.stdout 2> TOPP_IDMerger_1.stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'TOPP_IDMerger_1 failed\'; >&2 echo -e "stderr:\\n$(cat TOPP_IDMerger_1.stderr | sed \'s/^/ /\')"; echo -e "stdout:\\n$(cat TOPP_IDMerger_1.stdout)";fi\n+IDMerger -test -pepxml_protxml -in IDMerger_2_input1.idXML IDMerger_2_input2.idXML -out IDMerger_2_output.tmp > TOPP_IDMerger_2.stdout 2> TOPP_IDMerger_2.stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'TOPP_IDMerger_2 failed\'; >&2 echo -e "stderr:\\n$(cat TOPP_IDMerger_2.stderr | sed \'s/^/ /\')"; echo -e "stdout:\\n$(cat TOPP_IDMerger_2.stdout)";fi\n+IDMerger -test -in IDMerger_1_input1.idXML IDMerger_1_input1.idXML -out IDMerger_3_output.tmp > TOPP_IDMerger_3.stdout 2> TOPP_IDMerger_3.stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'TOPP_IDMerger_3 failed\'; >&2 echo -e "stderr:\\n$(cat TOPP_IDMerger_3.stderr | sed \'s/^/ /\')"; echo -e "stdout:\\n$(cat TOPP_IDMerger_3.stdout)";fi\n+IDMerger -test -in degenerated_empty.idXML degenerated_empty.idXML -out IDMerger_4_output.tmp > TOPP_IDMerger_4.stdout 2> TOPP_IDMerger_4.stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'TOPP_IDMerger_4 failed\'; >&2 echo -e "stderr:\\n$(cat TOPP_IDMerger_4.stderr | sed \'s/^/ /\')"; echo -e "stdout:\\n$(cat TOPP_IDMerger_4.stdout)";fi\n+IDMerger -test -in IDMerger_2_input1.idXML -add_to IDMerger_5_input1.idXML -out IDMerger_5_output.tmp > TOPP_IDMerger_5.stdout 2> TOPP_IDMerger_5.stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'TOPP_IDMerger_5 failed\'; >&2 echo -e "stderr:\\n$(cat TOPP_IDMerger_5.stderr | sed \'s/^/ /\')"; echo -e "stdout:\\n$(cat TOPP_IDMerger_5.stdout)";fi\n+BaselineFilter -test -in BaselineFilter_input.mzML -out BaselineFilter.tmp -struc_elem_length 1.5 > TOPP_BaselineFilter_1.stdout 2> TOPP_BaselineFilter_1.stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'TOPP_BaselineFilter_1 failed\'; >&2 echo -e "stderr:\\n$(cat TOPP_BaselineFilter_1.stderr | sed \'s/^/ /\')"; echo -e "stdout:\\n$(cat TOPP_BaselineFilter_1.stdout)";fi\n+ConsensusMapNormalizer -test -in ConsensusMapNormalizer_input.consensusXML -out ConsensusMapNormalizer.tmp > TOPP_ConsensusMapNormalizer_1.stdout 2> TOPP_ConsensusMapNormalizer_1.stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'TOPP_ConsensusMapNormalizer_1 failed\'; >&2 echo -e "stderr:\\n$(cat TOPP_ConsensusMapNormalizer_1.stderr | sed \'s/^/ /\')"; echo -e "stdout:\\n$(cat TOPP_ConsensusMapNormalizer_1.stdout)";fi\n+MapNormalizer -test -in MapNormalizer_input.mzML -out MapNormalizer.tmp > TOPP_MapNormalizer_1.stdout 2> TOPP_MapNormalizer_1.stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'TOPP_MapNormalizer_1 failed\'; >&2 echo -e "stderr:\\n$(cat TOPP_MapNormalizer_1.stderr | sed \'s/^/'..b'S_AssayGeneratorMetabo_9 failed\'; >&2 echo -e "stderr:\\n$(cat UTILS_AssayGeneratorMetabo_9.stderr | sed \'s/^/ /\')"; echo -e "stdout:\\n$(cat UTILS_AssayGeneratorMetabo_9.stdout)";fi\n+AssayGeneratorMetabo -test -executable "${SIRIUS_BINARY}" -in AssayGeneratorMetabo_input.mzML -in_id AssayGeneratorMetabo_ams_input.featureXML -out AssayGeneratorMetabo_ams_sirius_restrict_output.tmp.tsv -fragment_annotation sirius -use_exact_mass -transition_threshold 3.0 -min_transitions 2 -max_transitions 3 -min_fragment_mz 100 -max_fragment_mz 900 -preprocessing:filter_by_num_masstraces 1 -preprocessing:precursor_mz_tolerance 10 -preprocessing:precursor_mz_tolerance_unit ppm -preprocessing:feature_only -sirius:profile qtof -sirius:compound_timeout 100 > UTILS_AssayGeneratorMetabo_10.stdout 2> UTILS_AssayGeneratorMetabo_10.stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'UTILS_AssayGeneratorMetabo_10 failed\'; >&2 echo -e "stderr:\\n$(cat UTILS_AssayGeneratorMetabo_10.stderr | sed \'s/^/ /\')"; echo -e "stdout:\\n$(cat UTILS_AssayGeneratorMetabo_10.stdout)";fi\n+SiriusAdapter -test -executable "${SIRIUS_BINARY}" -in SiriusAdapter_2_input.mzML -in_featureinfo SiriusAdapter_2_input.featureXML -out_sirius SiriusAdapter_4_output.tmp -out_fingerid SiriusAdapter_4_foutput.tmp -sirius:auto_charge -sirius:profile qtof -sirius:database all > TOPP_SiriusAdapter_4.stdout 2> TOPP_SiriusAdapter_4.stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'TOPP_SiriusAdapter_4 failed\'; >&2 echo -e "stderr:\\n$(cat TOPP_SiriusAdapter_4.stderr | sed \'s/^/ /\')"; echo -e "stdout:\\n$(cat TOPP_SiriusAdapter_4.stdout)";fi\n+NovorAdapter -test -java_memory 512 -executable "${NOVOR_BINARY}" -in NovorAdapter_in.mzML -out NovorAdapter_1_out.tmp -variable_modifications "Acetyl (K)" -fixed_modifications "Carbamidomethyl (C)" -forbiddenResidues "I" > TOPP_NovorAdapter_1.stdout 2> TOPP_NovorAdapter_1.stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'TOPP_NovorAdapter_1 failed\'; >&2 echo -e "stderr:\\n$(cat TOPP_NovorAdapter_1.stderr | sed \'s/^/ /\')"; echo -e "stdout:\\n$(cat TOPP_NovorAdapter_1.stdout)";fi\n+FileConverter -test -force_TPP_compatibility -in spectra_spectrast.mzXML -out SpectrastAdapter_1_hack.mzML > TOPP_SpectrastSearchAdapter_0_prepare.stdout 2> TOPP_SpectrastSearchAdapter_0_prepare.stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'TOPP_SpectrastSearchAdapter_0_prepare failed\'; >&2 echo -e "stderr:\\n$(cat TOPP_SpectrastSearchAdapter_0_prepare.stderr | sed \'s/^/ /\')"; echo -e "stdout:\\n$(cat TOPP_SpectrastSearchAdapter_0_prepare.stdout)";fi\n+SpectraSTSearchAdapter -test -library_file testLib.splib -spectra_files SpectrastAdapter_1_hack.mzML -output_files SpectrastAdapter_1_out1.tmp.pep.xml -executable "${SPECTRAST_BINARY}" > TOPP_SpectrastSearchAdapter_1.stdout 2> TOPP_SpectrastSearchAdapter_1.stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'TOPP_SpectrastSearchAdapter_1 failed\'; >&2 echo -e "stderr:\\n$(cat TOPP_SpectrastSearchAdapter_1.stderr | sed \'s/^/ /\')"; echo -e "stdout:\\n$(cat TOPP_SpectrastSearchAdapter_1.stdout)";fi\n+SpectraSTSearchAdapter -test -library_file testLib.splib -spectra_files SpectrastAdapter_1_hack.mzML -output_files SpectrastAdapter_1_out1.tmp.pep.tsv -executable "${SPECTRAST_BINARY}" > TOPP_SpectrastSearchAdapter_2.stdout 2> TOPP_SpectrastSearchAdapter_2.stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'TOPP_SpectrastSearchAdapter_2 failed\'; >&2 echo -e "stderr:\\n$(cat TOPP_SpectrastSearchAdapter_2.stderr | sed \'s/^/ /\')"; echo -e "stdout:\\n$(cat TOPP_SpectrastSearchAdapter_2.stdout)";fi\n+LuciphorAdapter -test -in LuciphorAdapter_1_input.mzML -java_memory 1024 -id LuciphorAdapter_1_input.idXML -out LuciphorAdapter_1_output.tmp -executable "${LUCIPHOR_BINARY}" -min_num_psms_model 1 > TOPP_LuciphorAdapter_1.stdout 2> TOPP_LuciphorAdapter_1.stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'TOPP_LuciphorAdapter_1 failed\'; >&2 echo -e "stderr:\\n$(cat TOPP_LuciphorAdapter_1.stderr | sed \'s/^/ /\')"; echo -e "stdout:\\n$(cat TOPP_LuciphorAdapter_1.stdout)";fi\n' |
| b |
| diff -r eb22f145fae1 -r 51b9c2d5b4c3 prepare_test_data_manual.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/prepare_test_data_manual.sh Wed Sep 09 12:55:31 2020 +0000 |
| [ |
| b'@@ -0,0 +1,155 @@\n+MSSimulator -test -in DecoyDatabase_1.fasta -out MSsimulator.mzml -algorithm:RandomNumberGenerators:biological reproducible -algorithm:RandomNumberGenerators:technical reproducible > MSSimulator_1.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'MSSimulator_1 failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+MSSimulator -test -in DecoyDatabase_1.fasta -out MSsimulator_MALDI.mzml -algorithm:RandomNumberGenerators:biological reproducible -algorithm:RandomNumberGenerators:technical reproducible -algorithm:MSSim:Global:ionization_type MALDI > MSSimulator_2.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'MSSimulator_2 failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+ClusterMassTracesByPrecursor -test -in_ms1 ConsensusMapNormalizer_input.consensusXML -in_swath ConsensusMapNormalizer_input.consensusXML -out ClusterMassTracesByPrecursor.mzml > ClusterMassTracesByPrecursor.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'ClusterMassTracesByPrecursor failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+ClusterMassTraces -test -in ConsensusMapNormalizer_input.consensusXML -out ClusterMassTraces.mzml > ClusterMassTraces.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'ClusterMassTraces failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+CVInspector -test -cv_files CHEMISTRY/XLMOD.obo -cv_names XLMOD -mapping_file MAPPING/ms-mapping.xml -html CVInspector.html > CVInspector.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'CVInspector failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+DeMeanderize -test -in MSsimulator_MALDI.mzml -out DeMeanderize.mzml > DeMeanderize.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'DeMeanderize failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+# TODO DigestorMotif\n+\n+Digestor -test -in random.fa -out Digestor.fasta -out_type fasta > Digestor.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'Digestor failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+EICExtractor -test -in spectra.mzML -pos FileConverter_10_input.edta -out EICExtractor.csv > EICExtractor.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'EICExtractor failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+#TODO ERPairFinder\n+\n+FeatureFinderIsotopeWavelet -test -in FeatureFinderCentroided_1_input.mzML -out FeatureFinderIsotopeWavelet.featureXML > FeatureFinderIsotopeWavelet.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'FeatureFinderIsotopeWavelet failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+\n+FFEval -test -in FeatureFinderCentroided_1_output.featureXML -truth FeatureFinderCentroided_1_output.featureXML -out FFEval.featureXML -out_roc FFEval_roc.csv > FFEval.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'FFEval failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+# TODO? deprecated IDDecoyProbability\n+\n+IDExtractor -test -in MSGFPlusAdapter_1_out.idXML -best_hits -number_of_peptides 1 -out IDExtractor.idXML > IDExtractor.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'IDExtractor failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+LabeledEval -test -in FeatureLinkerLabeled_1_input.featureXML -truth FeatureLinkerLabeled_1_output.consensusXML> LabeledEval.txt > LabeledEval.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'LabeledEval failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+MapStatistics -test -in SiriusAdapter_3_input.featureXML -out MapStatistics.txt > MapStatistics_1.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'MapStatistics_1 failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+MapStatistics -test -in ConsensusXMLFile_1.consensusXML -out MapStatistics2.txt > MapStatistics_2.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'MapStatistics_2 failed\'; '..b'\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+# TODO out should be tsv, but needs https://github.com/OpenMS/OpenMS/pull/4533\n+RTEvaluation -in PeptideIndexer_1.idXML -out RTEvaluation.csv > RTEvaluation.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'RTEvaluation failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+ln -fs RTEvaluation.csv RTEvaluation.tsv > .stdout 2> stderr\n+\n+SemanticValidator -test -in FileFilter_1_input.mzML -mapping_file MAPPING/ms-mapping.xml > SemanticValidator.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'SemanticValidator failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+IDFilter -in PeptideIndexer_1.idXML -best:strict -out SequenceCoverageCalculator_1.idXML > IDFilter.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'IDFilter failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+SequenceCoverageCalculator -test -in_database PeptideIndexer_1.fasta -in_peptides SequenceCoverageCalculator_1.idXML -out SequenceCoverageCalculator.txt > SequenceCoverageCalculator.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'SequenceCoverageCalculator failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+# TODO SpecLibCreator\n+\n+SpectraFilterBernNorm -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterBernNorm.mzML > SpectraFilterBernNorm.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'SpectraFilterBernNorm failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+SpectraFilterMarkerMower -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterMarkerMower.mzML > SpectraFilterMarkerMower.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'SpectraFilterMarkerMower failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+SpectraFilterNLargest -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterNLargest.mzML > SpectraFilterNLargest.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'SpectraFilterNLargest failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+SpectraFilterNormalizer -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterNormalizer.mzML > SpectraFilterNormalizer.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'SpectraFilterNormalizer failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+SpectraFilterParentPeakMower -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterParentPeakMower.mzML > SpectraFilterParentPeakMower.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'SpectraFilterParentPeakMower failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+SpectraFilterScaler -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterScaler.mzML > SpectraFilterScaler.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'SpectraFilterScaler failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+SpectraFilterThresholdMower -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterThresholdMower.mzML > SpectraFilterThresholdMower.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'SpectraFilterThresholdMower failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+SpectraMerger -test -in NovorAdapter_in.mzML -out SpectraMerger_1.mzML > SpectraMerger.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'SpectraMerger failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+# TODO SvmTheoreticalSpectrumGeneratorTrainer\n+\n+TransformationEvaluation -test -in FileInfo_16_input.trafoXML -out TransformationEvaluation.trafoXML > TransformationEvaluation.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'TransformationEvaluation failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n+\n+XMLValidator -test -in FileFilter_1_input.mzML > XMLValidator.stdout 2> stderr\n+if [[ "$?" -ne "0" ]]; then >&2 echo \'XMLValidator failed\'; >&2 echo -e "stderr:\\n$(cat stderr | sed \'s/^/ /\')"; fi\n' |
| b |
| diff -r eb22f145fae1 -r 51b9c2d5b4c3 readme.md --- a/readme.md Fri May 17 10:26:11 2019 -0400 +++ b/readme.md Wed Sep 09 12:55:31 2020 +0000 |
| [ |
| b'@@ -8,175 +8,127 @@\n More informations are available at:\n \n * https://github.com/OpenMS/OpenMS\n- * http://open-ms.sourceforge.net\n+ * https://www.openms.de/\n+\n+The wrappers for these tools and most of their tests are automatically\n+generated using the `generate.sh` script. The generation of the tools is\n+based on the CTDConverter (https://github.com/WorkflowConversion/CTDConverter)\n+which can be fine tuned via the `hardcoded_params.json` file. This file allows\n+to blacklist and hardcode parameters and to modify or set arbitrary\n+CTD/XML attributes.\n+\n+Note that, due to its size, the test data is excluded from this repository. In\n+order to generate the test data on call `test-data.sh`.\n+\n+Manual updates should only be done to\n+\n+- the `@GALAXY_VERSION@"` token in `macros.xml`\n+- and the manually contributed tests in `macros_test.xml` (The goal is that all\n+ tools that do not have an automatically generated test are covered here)\n+- the `hardcoded_params.json` files\n+\n+In a few cases patches may be acceptable.\n+\n+Installation\n+============\n+\n+The Galaxy OpenMS tools can be installed from the toolshed. While most tools\n+will work out of the box some need attention since requirements can not be\n+fulfilled via Conda:\n+\n+Not yet in Conda are:\n+\n+- SpectraST (http://tools.proteomecenter.org/wiki/index.php?title=SpectraST)\n+- MaRaCluster (https://github.com/statisticalbiotechnology/maracluster)\n+\n+Binaries for these tools can easily be obtained via: \n+\n+```\n+VERSION=....\n+git git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git OpenMS$VERSION.0-git\n+git submodule init OpenMS$VERSION.0-git\n+git submodule update OpenMS$VERSION.0-git\n+```\n+\n+They are located in `OpenMS$VERSION-git/THIRDPARTY/`. \n \n+Not in Conda due to licencing restrictions:\n+\n+- Mascot http://www.matrixscience.com/\n+- MSFragger https://github.com/Nesvilab/MSFragger\n+- Novor http://www.rapidnovor.org/novor\n+\n+There are multiple ways to enable the Galaxy tools to use these binaries. \n+\n+- Just copy them to the `bin` path within Galaxy\'s conda environment\n+- Put them in any other path that that is included in PATH\n+- Edit the corresponding tools: In the command line part search for the parameters `-executable`, `-maracluster_executable`, or `-mascot_directory` and edit them appropriately.\n+\n+Working\n+=======\n+\n+The tools work by:\n+\n+Preprocessing:\n+\n+- For each input / output data set parameter a directory is crated (named by\n+ the parameter)\n+- For input data set parameters the links to the actual location of the data\n+ sets are created\n+\n+Main:\n+\n+- The galaxy wrapper create two json config files: one containing the\n+ parameters and the values chosen by the user and the other the values of\n+ hardcoded parameters.\n+- With `OpenMSTool -write_ctd ./` a CTD (names OpenMSTool.ctd) file is\n+ generated that contains the default values.\n+- A call to `fill_ctd.py` fills in the values from the json config files into\n+ the CTD file\n+- The actual tool is called `OpenMSTool -ini OpenMSTool.ctd` and also all input\n+ and output parameters are given on the command line.\n+\n+Postprocessing:\n+\n+- output data sets are moved to the final locations\n+\n+Note: The reason for handling data sets on the command line (and not specifying\n+them in the CTD file) is mainly that all files in Galaxy have the extension\n+`.dat` and OpenMS tools require an appropriate extension. But this may change\n+in the future.\n \n Generating OpenMS wrappers\n ==========================\n \n- * install OpenMS (you can do this automatically through Conda)\n- * create a folder called CTD\n- * if you installed openms as a binary in a specific directory, execute the following command in the `openms/bin` directory:\n- \n- ```bash\n- for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done;\n- ```\n- \n- * if there is no binary release (e.g. as with version 2.2), download and unpack the Conda package, find the `bin` folder and create a list of the tools as follow:\n- \n- ```bash\n- ls '..b'yrimatch\' wrappers/MyriMatchAdapter.xml\n- sed -i \'13 a\\-omssa_executable omssa\' wrappers/OMSSAAdapter.xml\n- sed -i \'13 a\\-xtandem_executable xtandem\' wrappers/XTandemAdapter.xml\n- ```\n- \n- * For some tools, additional work has to be done. In `MSGFPlusAdapter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where):\n- \n- ```\n- <command><![CDATA[\n-\n- ## check input file type\n- #set $in_type = $param_in.ext\n+2. The CI testing framework of OpenMS contains command lines and test data \n+ (https://github.com/OpenMS/OpenMS/tree/develop/src/tests/topp). These tests\n+ are described in two CMake files.\n \n- ## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files\n- ln -s \'$param_in\' \'param_in.${in_type}\' &&\n- ln -s \'$param_database\' param_database.fasta &&\n- ## find location of the MSGFPlus.jar file of the msgf_plus conda package\n- MSGF_JAR=\\$(msgf_plus -get_jar_path) &&\n+ - From these CMake files Galaxy tests are auto generated and stored in `macros_autotest.xml`\n+ - The command lines are stored in `prepare_test_data.sh` for regeneration of test data\n+\n+More details can be found in the comments of the shell script.\n+\n+Open problems\n+=============\n \n- MSGFPlusAdapter\n- -executable \\$MSGF_JAR\n- #if $param_in:\n- -in \'param_in.${in_type}\'\n- #end if\n- #if $param_out:\n- -out $param_out\n- #end if\n- #if $param_mzid_out:\n- -mzid_out $param_mzid_out\n- #end if\n- #if $param_database:\n- -database param_database.fasta\n- #end if\n- \n- [...]\n- ]]>\n- ```\n- \n- * In Xtandem Converter and probably in others:\n- \n- ```\n- #if str($param_missed_cleavages) != \'\':\n- ```\n- This is because integers needs to be compared as string otherwise `0` becomes `false`.\n- \n- * In `MetaProSIP.xml` add `R` as a requirement:\n- \n- ```\n- <expand macro="requirements">\n- <requirement type="package" version="3.3.1">r-base</requirement>\n- </expand>\n- ```\n- \n- * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where):\n- \n- ```\n- <command><![CDATA[\n- \n- ## check input file type\n- #set $in_type = $param_in.ext\n+Some tools stall in CI testing using `--biocontainers` which is why the OpenMS\n+tools are currently listed in `.tt_biocontainer_skip`. This is\n \n- ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files\n- ln -s \'$param_in\' \'param_in.${in_type}\' &&\n-\n- IDFileConverter\n-\n- #if $param_in:\n- -in \'param_in.${in_type}\'\n- #end if\n-\n- [...]\n- ]]>\n- ```\n+- AssayGeneratorMetabo and SiriusAdapter (both depend on sirius)\n+- OMSSAAdapter\n \n- * In `IDFileConverter.xml` and `FileConverter.xml` add `auto_format="true"` to the output, e.g.:\n- \n- - `<data name="param_out" auto_format="true"/>`\n- - `<data name="param_out" metadata_source="param_in" auto_format="true"/>`\n- \n- * To add an example test case to `DecoyDatabase.xml` add the following after the output section. If standard settings change you might have to adjust the options and/or the test files.\n- \n- ```\n- <tests>\n- <test>\n- <param name="param_in" value="DecoyDatabase_input.fasta"/>\n- <output name="param_out" file="DecoyDatabase_output.fasta"/>\n- </test>\n- </tests>\n- ```\n- \n- * Additionally cause of lacking dependencies, the following adapters have been removed in `SKIP_TOOLS_FILES.txt` as well:\n- * OMSSAAdapter\n- * MyrimatchAdapter\n- \n- * Additionally cause of a problematic parameter (-model_directory), the following adapter has been removed:\n- * PepNovoAdapter\n-\n+Using `docker -t` seems to solve the problem (see\n+https://github.com/galaxyproject/galaxy/issues/10153).\n \n Licence (MIT)\n =============\n' |
| b |
| diff -r eb22f145fae1 -r 51b9c2d5b4c3 test-data.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data.sh Wed Sep 09 12:55:31 2020 +0000 |
| [ |
| b'@@ -0,0 +1,255 @@\n+#!/usr/bin/env bash\n+\n+VERSION=2.5\n+FILETYPES="filetypes.txt"\n+CONDAPKG="https://anaconda.org/bioconda/openms/2.5.0/download/linux-64/openms-2.5.0-h463af6b_1.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+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="$tmp/CTDConverter"\n+\n+\n+if type conda > /dev/null; then \n+\ttrue\n+else\n+\twget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh\n+\tbash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda"\n+\tsource "$tmp/miniconda/bin/activate"\n+fi\n+eval "$(conda shell.bash hook)"\n+\n+if [[ -z "$1" ]]; then\n+\tautotests="/dev/null"\n+else\n+\tautotests="$1"\n+fi\n+\n+###############################################################################\n+## get \n+## - conda environment (for executing the binaries) and \n+## - the git clone of OpenMS (for generating the tests)\n+###############################################################################\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+else\n+\tcd $OPENMSGIT\n+\t\tgit pull origin release/$VERSION.0\n+\tcd -\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+else\n+\tconda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -p $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION openjdk=8.0.192 ctdopts=1.4 lxml\n+# chmod -R u-w $OPENMSENV \n+fi\n+###############################################################################\n+## get the \n+## - conda package (for easy access and listing of the OpenMS binaries), \n+###############################################################################\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+fi\n+\n+###############################################################################\n+## Get python libaries for CTD -> Galaxy conversion\n+## TODO fix to main repo OR conda packkage if PRs are merged \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+else\n+\tcd $CTDCONVERTER\n+\tgit pull origin topic/cdata\n+\tcd -\n+fi\n+export PYTHONPATH=$(pwd)/CTDopts\n+\n+###############################################################################\n+## copy all the test data files to test-data\n+## most of it (outputs) will be overwritten later, but its needed for\n+## prepare_test_data\n+###############################################################################\n+echo "Get test data"\n+cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/\n+cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/\n+cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/\n+cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/\n+if [[ ! -f test-data/MetaboliteSpectralDB.mzML ]]; then \n+\twget -q https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML && mv MetaboliteSpectralDB.mzML test-data/\n+fi\n+ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt\n+ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv\n+\n+if [ ! -d test-data/pepno'..b'e results for the tests and run it\n+###############################################################################\n+echo "Create test shell script"\n+\n+echo -n "" > prepare_test_data.sh\n+echo \'export COMET_BINARY="comet"\' >> prepare_test_data.sh\n+echo \'export CRUX_BINARY="crux"\' >> prepare_test_data.sh\n+echo \'export FIDOCHOOSEPARAMS_BINARY="FidoChooseParameters"\' >> prepare_test_data.sh\n+echo \'export FIDO_BINARY="Fido"\' >> prepare_test_data.sh\n+echo \'export LUCIPHOR_BINARY="$(dirname $(realpath $(which luciphor2)))/luciphor2.jar"\' >> prepare_test_data.sh\n+\n+echo \'export MARACLUSTER_BINARY="\'"$OPENMSGIT"\'/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster"\'>> prepare_test_data.sh\n+echo \'export MSFRAGGER_BINARY="/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar"\'>> prepare_test_data.sh\n+echo \'export MSGFPLUS_BINARY="$(msgf_plus -get_jar_path)"\' >> prepare_test_data.sh\n+echo \'export MYRIMATCH_BINARY="myrimatch"\'>> prepare_test_data.sh\n+echo \'export NOVOR_BINARY="/home/berntm/Downloads/novor/lib/novor.jar"\' >> prepare_test_data.sh\n+echo \'export OMSSA_BINARY="$(dirname $(realpath $(which omssacl)))/omssacl"\'>> prepare_test_data.sh\n+echo \'export PERCOLATOR_BINARY="percolator"\'>> prepare_test_data.sh\n+echo \'export SIRIUS_BINARY="$(which sirius)"\' >> prepare_test_data.sh\n+echo \'export SPECTRAST_BINARY="spectrast"\' >> prepare_test_data.sh\n+echo \'export XTANDEM_BINARY="xtandem"\' >> prepare_test_data.sh\n+echo \'export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"\' >> prepare_test_data.sh\n+\n+prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh\n+\n+# prepare_test_data > tmp_test_data.sh\n+# # remove calls not needed for the tools listed in any .list file\n+# echo LIST $LIST\n+# if [ ! -z "$LIST" ]; then\n+# \tREX=$(echo $LIST | sed \'s/ /\\n/g\' | sed \'s@.*/\\([^/]\\+\\).xml$@\\1@\' | tr \'\\n\' \'|\' | sed \'s/|$//\')\n+# else\n+# \tREX=".*"\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+cd ./test-data || exit\n+../prepare_test_data.sh\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+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+\n+\n+# # # exit\n+\n+###############################################################################\n+## auto generate tests\n+###############################################################################\n+\n+echo "Write test macros to "$autotests\n+echo "<macros>" > $autotests\n+for i in $(ls *xml |grep -v macros)\n+do\n+\tb=$(basename "$i" .xml)\n+\tget_tests2 "$b" >> $autotests \n+done\n+echo "</macros>" >> $autotests\n+\n+echo "Create test data links"\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+if [[ ! -z "$1" ]]; then\n+\techo "" > macros_discarded_auto.xml\n+\tfor i in OpenSwathFileSplitter IDRipper MzMLSplitter\n+\tdo\n+\t\techo "<xml name=\\"manutest_$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 "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' |
| b |
| diff -r eb22f145fae1 -r 51b9c2d5b4c3 tool-data/pepnovo_models.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/pepnovo_models.loc.sample Wed Sep 09 12:55:31 2020 +0000 |
| b |
| @@ -0,0 +1,23 @@ +# This is a sample file distributed with Galaxy that enables tools +# to use pepnovo models +# The file has three tab separated columns: name, value, and path. +# The idea is that there are a number of models in a directory: +# - each model directory has a unique name (columns 2 and 0) +# - each model can contain a set of models (column 1) +# +# The following example works fo the default models from +# http://proteomics.ucsd.edu/Software/PepNovo.html (just remove the comment +# chars and replace DIR_TO_PEPNOVO_MODELS) + +#default_models CID_IT_TRYP DIR_TO_PEPNOVO_MODELS +#default_models LTQ_COMP DIR_TO_PEPNOVO_MODELS +#default_models DBC4_PEAK DIR_TO_PEPNOVO_MODELS +#default_models CID_IT_TRYP_TAG5 DIR_TO_PEPNOVO_MODELS +#default_models CID_IT_TRYP_TAG6 DIR_TO_PEPNOVO_MODELS +#default_models ITDNV_PEAK DIR_TO_PEPNOVO_MODELS +#default_models CID_IT_TRYP_SCORE DIR_TO_PEPNOVO_MODELS +#default_models CID_IT_TRYP_TAG3 DIR_TO_PEPNOVO_MODELS +#default_models CID_IT_TRYP_DNVPART DIR_TO_PEPNOVO_MODELS +#default_models CID_IT_TRYP_TAG4 DIR_TO_PEPNOVO_MODELS +#default_models CID_IT_TRYP_DB DIR_TO_PEPNOVO_MODELS +#default_models CID_IT_TRYP_CSP DIR_TO_PEPNOVO_MODELS |
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| diff -r eb22f145fae1 -r 51b9c2d5b4c3 tool.conf --- a/tool.conf Fri May 17 10:26:11 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,160 +0,0 @@ -<?xml version='1.0' encoding='UTF-8'?> -<toolbox> - <section id="section-id-Peptidepropertyprediction" name="Peptide property prediction"> - <tool file="openms/PTModel.xml"/> - <tool file="openms/PTPredict.xml"/> - <tool file="openms/RTModel.xml"/> - <tool file="openms/RTPredict.xml"/> - </section> - <section id="section-id-TargetedExperiments" name="Targeted Experiments"> - <tool file="openms/InclusionExclusionListCreator.xml"/> - <tool file="openms/MRMMapper.xml"/> - <tool file="openms/OpenSwathAnalyzer.xml"/> - <tool file="openms/OpenSwathAssayGenerator.xml"/> - <tool file="openms/OpenSwathChromatogramExtractor.xml"/> - <tool file="openms/OpenSwathConfidenceScoring.xml"/> - <tool file="openms/OpenSwathDecoyGenerator.xml"/> - <tool file="openms/OpenSwathDIAPreScoring.xml"/> - <tool file="openms/OpenSwathFeatureXMLToTSV.xml"/> - <tool file="openms/OpenSwathFileSplitter.xml"/> - <tool file="openms/OpenSwathMzMLFileCacher.xml"/> - <tool file="openms/OpenSwathRewriteToFeatureXML.xml"/> - <tool file="openms/OpenSwathRTNormalizer.xml"/> - <tool file="openms/PrecursorIonSelector.xml"/> - <tool file="openms/TargetedFileConverter.xml"/> - </section> - <section id="section-id-Utilities" name="Utilities"> - <tool file="openms/AccurateMassSearch.xml"/> - <tool file="openms/CVInspector.xml"/> - <tool file="openms/DatabaseFilter.xml"/> - <tool file="openms/DecoyDatabase.xml"/> - <tool file="openms/DeMeanderize.xml"/> - <tool file="openms/Digestor.xml"/> - <tool file="openms/DigestorMotif.xml"/> - <tool file="openms/ERPairFinder.xml"/> - <tool file="openms/FFEval.xml"/> - <tool file="openms/FuzzyDiff.xml"/> - <tool file="openms/IDDecoyProbability.xml"/> - <tool file="openms/IDExtractor.xml"/> - <tool file="openms/IDMassAccuracy.xml"/> - <tool file="openms/IDScoreSwitcher.xml"/> - <tool file="openms/IDSplitter.xml"/> - <tool file="openms/LabeledEval.xml"/> - <tool file="openms/LowMemPeakPickerHiRes.xml"/> - <tool file="openms/LowMemPeakPickerHiRes_RandomAccess.xml"/> - <tool file="openms/MassCalculator.xml"/> - <tool file="openms/MetaboliteSpectralMatcher.xml"/> - <tool file="openms/MetaProSIP.xml"/> - <tool file="openms/MRMPairFinder.xml"/> - <tool file="openms/MRMTransitionGroupPicker.xml"/> - <tool file="openms/MSSimulator.xml"/> - <tool file="openms/MultiplexResolver.xml"/> - <tool file="openms/MzMLSplitter.xml"/> - <tool file="openms/OpenSwathWorkflow.xml"/> - <tool file="openms/QCCalculator.xml"/> - <tool file="openms/QCEmbedder.xml"/> - <tool file="openms/QCExporter.xml"/> - <tool file="openms/QCExtractor.xml"/> - <tool file="openms/QCImporter.xml"/> - <tool file="openms/QCMerger.xml"/> - <tool file="openms/QCShrinker.xml"/> - <tool file="openms/RNPxl.xml"/> - <tool file="openms/RNPxlSearch.xml"/> - <tool file="openms/RNPxlXICFilter.xml"/> - <tool file="openms/RTEvaluation.xml"/> - <tool file="openms/SemanticValidator.xml"/> - <tool file="openms/SequenceCoverageCalculator.xml"/> - <tool file="openms/SimpleSearchEngine.xml"/> - <tool file="openms/SpecLibCreator.xml"/> - <tool file="openms/SpectraSTSearchAdapter.xml"/> - <tool file="openms/SvmTheoreticalSpectrumGeneratorTrainer.xml"/> - <tool file="openms/TICCalculator.xml"/> - <tool file="openms/TopPerc.xml"/> - <tool file="openms/TransformationEvaluation.xml"/> - <tool file="openms/XMLValidator.xml"/> - </section> - <section id="section-id-MapAlignment" name="Map Alignment"> - <tool file="openms/ConsensusMapNormalizer.xml"/> - <tool file="openms/FeatureLinkerLabeled.xml"/> - <tool file="openms/FeatureLinkerUnlabeled.xml"/> - <tool file="openms/FeatureLinkerUnlabeledKD.xml"/> - <tool file="openms/FeatureLinkerUnlabeledQT.xml"/> - <tool file="openms/MapRTTransformer.xml"/> - </section> - <section id="section-id-IDProcessing" name="ID Processing"> - <tool file="openms/ConsensusID.xml"/> - <tool file="openms/FalseDiscoveryRate.xml"/> - <tool file="openms/FidoAdapter.xml"/> - <tool file="openms/IDConflictResolver.xml"/> - <tool file="openms/IDFileConverter.xml"/> - <tool file="openms/IDFilter.xml"/> - <tool file="openms/IDMapper.xml"/> - <tool file="openms/IDPosteriorErrorProbability.xml"/> - <tool file="openms/IDRTCalibration.xml"/> - <tool file="openms/LuciphorAdapter.xml"/> - <tool file="openms/PeptideIndexer.xml"/> - <tool file="openms/PhosphoScoring.xml"/> - </section> - <section id="section-id-Signalprocessingandpreprocessing" name="Signal processing and preprocessing"> - <tool file="openms/BaselineFilter.xml"/> - <tool file="openms/ExternalCalibration.xml"/> - <tool file="openms/HighResPrecursorMassCorrector.xml"/> - <tool file="openms/InternalCalibration.xml"/> - <tool file="openms/MapNormalizer.xml"/> - <tool file="openms/MassTraceExtractor.xml"/> - <tool file="openms/NoiseFilterGaussian.xml"/> - <tool file="openms/NoiseFilterSGolay.xml"/> - <tool file="openms/PeakPickerHiRes.xml"/> - <tool file="openms/PeakPickerIterative.xml"/> - <tool file="openms/PeakPickerWavelet.xml"/> - <tool file="openms/PrecursorMassCorrector.xml"/> - <tool file="openms/SpectraMerger.xml"/> - <tool file="openms/TOFCalibration.xml"/> - </section> - <section id="section-id-Identification" name="Identification"> - <tool file="openms/CompNovoCID.xml"/> - <tool file="openms/CompNovo.xml"/> - <tool file="openms/InspectAdapter.xml"/> - <tool file="openms/MascotAdapter.xml"/> - <tool file="openms/MascotAdapterOnline.xml"/> - <tool file="openms/MSGFPlusAdapter.xml"/> - <tool file="openms/ProteinInference.xml"/> - <tool file="openms/SpectraFilterBernNorm.xml"/> - <tool file="openms/SpectraFilterMarkerMower.xml"/> - <tool file="openms/SpectraFilterNLargest.xml"/> - <tool file="openms/SpectraFilterNormalizer.xml"/> - <tool file="openms/SpectraFilterParentPeakMower.xml"/> - <tool file="openms/SpectraFilterScaler.xml"/> - <tool file="openms/SpectraFilterSqrtMower.xml"/> - <tool file="openms/SpectraFilterThresholdMower.xml"/> - <tool file="openms/SpectraFilterWindowMower.xml"/> - <tool file="openms/XTandemAdapter.xml"/> - </section> - <section id="section-id-FileHandling" name="File Handling"> - <tool file="openms/DTAExtractor.xml"/> - <tool file="openms/FileConverter.xml"/> - <tool file="openms/FileFilter.xml"/> - <tool file="openms/FileInfo.xml"/> - <tool file="openms/FileMerger.xml"/> - <tool file="openms/IDMerger.xml"/> - <tool file="openms/IDRipper.xml"/> - <tool file="openms/MapStatistics.xml"/> - <tool file="openms/MzTabExporter.xml"/> - <tool file="openms/TextExporter.xml"/> - </section> - <section id="section-id-Quantitation" name="Quantitation"> - <tool file="openms/AdditiveSeries.xml"/> - <tool file="openms/Decharger.xml"/> - <tool file="openms/EICExtractor.xml"/> - <tool file="openms/FeatureFinderCentroided.xml"/> - <tool file="openms/FeatureFinderIdentification.xml"/> - <tool file="openms/FeatureFinderIsotopeWavelet.xml"/> - <tool file="openms/FeatureFinderMetabo.xml"/> - <tool file="openms/FeatureFinderMRM.xml"/> - <tool file="openms/FeatureFinderMultiplex.xml"/> - <tool file="openms/FeatureFinderSuperHirn.xml"/> - <tool file="openms/IsobaricAnalyzer.xml"/> - <tool file="openms/ProteinQuantifier.xml"/> - <tool file="openms/ProteinResolver.xml"/> - </section> -</toolbox> |
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| diff -r eb22f145fae1 -r 51b9c2d5b4c3 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Sep 09 12:55:31 2020 +0000 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of pepnovo models --> + <table name="pepnovo_models" comment_char="#" allow_duplicate_entries="False"> + <columns>name,value,path</columns> + <file path="tool-data/pepnovo_models.loc" /> + </table> +</tables> |
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| diff -r eb22f145fae1 -r 51b9c2d5b4c3 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Sep 09 12:55:31 2020 +0000 |
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| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all eggnog_mapper data --> + <table name="pepnovo_models" comment_char="#"> + <columns>name,value,path</columns> + <file path="${__HERE__}/test-data/pepnovo_models.loc" /> + </table> +</tables> |
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| diff -r eb22f145fae1 -r 51b9c2d5b4c3 tools_blacklist.txt --- a/tools_blacklist.txt Fri May 17 10:26:11 2019 -0400 +++ b/tools_blacklist.txt Wed Sep 09 12:55:31 2020 +0000 |
| b |
| @@ -1,9 +1,24 @@ -OMSSAAdapter -MyriMatchAdapter -PepNovoAdapter -SeedListGenerator -SpecLibSearcher -MapAlignerIdentification -MapAlignerPoseClustering -MapAlignerSpectrum -MapAlignerRTTransformer +# 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 + +# seems currently unusable https://github.com/OpenMS/OpenMS/pull/4443 +OpenSwathDIAPreScoring + +# https://github.com/OpenMS/OpenMS/issues/4550#issuecomment-594065727 +ProteomicsLFQ + +# https://github.com/OpenMS/OpenMS/issues/4401 +InclusionExclusionListCreator +RTPredict +PTPredict |