| Previous changeset 7:7911914e96f6 (2020-09-09) Next changeset 9:3dc6d9795d5b (2020-10-13) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f5fcdd54599554099fb00b1973cc91a766ad246a" |
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modified:
RNPxlSearch.xml fill_ctd.py generate.sh hardcoded_params.json macros_autotest.xml macros_discarded_auto.xml macros_test.xml test-data.sh |
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added:
404-urls.patch |
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| diff -r 7911914e96f6 -r 25cc460f9092 404-urls.patch --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/404-urls.patch Wed Sep 23 15:03:39 2020 +0000 |
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| @@ -0,0 +1,65 @@ +diff -ruN ClusterMassTracesByPrecursor.xml ClusterMassTracesByPrecursor.xml +--- ClusterMassTracesByPrecursor.xml 2020-09-21 17:02:36.060104555 +0200 ++++ ClusterMassTracesByPrecursor.xml 2020-09-21 17:00:02.864815223 +0200 +@@ -75,8 +75,6 @@ + <expand macro="manutest_ClusterMassTracesByPrecursor"/> + </tests> + <help><![CDATA[Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile. +- +- +-For more information, visit http://www.openms.de/documentation/UTILS_ClusterMassTracesByPrecursor.html]]></help> ++]]></help> + <expand macro="references"/> + </tool> +diff -ruN ClusterMassTraces.xml ClusterMassTraces.xml +--- ClusterMassTraces.xml 2020-09-21 17:02:36.060104555 +0200 ++++ ClusterMassTraces.xml 2020-09-21 17:00:22.192722036 +0200 +@@ -69,8 +69,6 @@ + <expand macro="manutest_ClusterMassTraces"/> + </tests> + <help><![CDATA[Creates pseudo spectra. +- +- +-For more information, visit http://www.openms.de/documentation/UTILS_ClusterMassTraces.html]]></help> ++]]></help> + <expand macro="references"/> + </tool> +diff -ruN FeatureFinderSuperHirn.xml FeatureFinderSuperHirn.xml +--- FeatureFinderSuperHirn.xml 2020-09-21 17:02:36.060104555 +0200 ++++ FeatureFinderSuperHirn.xml 2020-09-21 17:00:42.372625907 +0200 +@@ -103,8 +103,6 @@ + <expand macro="manutest_FeatureFinderSuperHirn"/> + </tests> + <help><![CDATA[Finds mass spectrometric features in mass spectra. +- +- +-For more information, visit http://www.openms.de/documentation/TOPP_FeatureFinderSuperHirn.html]]></help> ++]]></help> + <expand macro="references"/> + </tool> +diff -ruN MSFraggerAdapter.xml MSFraggerAdapter.xml +--- MSFraggerAdapter.xml 2020-09-21 17:02:36.060104555 +0200 ++++ MSFraggerAdapter.xml 2020-09-21 17:01:04.892519985 +0200 +@@ -250,8 +250,6 @@ + <expand macro="manutest_MSFraggerAdapter"/> + </tests> + <help><![CDATA[Peptide Identification with MSFragger +- +- +-For more information, visit http://www.openms.de/documentation/UTILS_MSFraggerAdapter.html]]></help> ++]]></help> + <expand macro="references"/> + </tool> +diff -ruN SimpleSearchEngine.xml SimpleSearchEngine.xml +--- SimpleSearchEngine.xml 2020-09-21 17:02:36.060104555 +0200 ++++ SimpleSearchEngine.xml 2020-09-21 17:01:33.020389600 +0200 +@@ -5373,8 +5373,6 @@ + <expand macro="manutest_SimpleSearchEngine"/> + </tests> + <help><![CDATA[Annotates MS/MS spectra using SimpleSearchEngine. +- +- +-For more information, visit http://www.openms.de/documentation/UTILS_SimpleSearchEngine.html]]></help> ++]]></help> + <expand macro="references"/> + </tool> |
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| diff -r 7911914e96f6 -r 25cc460f9092 RNPxlSearch.xml --- a/RNPxlSearch.xml Wed Sep 09 19:56:16 2020 +0000 +++ b/RNPxlSearch.xml Wed Sep 23 15:03:39 2020 +0000 |
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| @@ -5327,35 +5327,35 @@ <option value="Trypsin/P">Trypsin/P</option> <option value="V8-DE">V8-DE</option> <option value="Trypsin" selected="true">Trypsin</option> - <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> - <option value="Alpha-lytic protease">Alpha-lytic protease</option> - <option value="2-iodobenzoate">2-iodobenzoate</option> - <option value="iodosobenzoate">iodosobenzoate</option> - <option value="staphylococcal protease/D">staphylococcal protease/D</option> - <option value="Lys-C/P">Lys-C/P</option> - <option value="PepsinA">PepsinA</option> - <option value="Arg-C/P">Arg-C/P</option> - <option value="Asp-N">Asp-N</option> - <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> <option value="Glu-C+P">Glu-C+P</option> <option value="PepsinA + P">PepsinA + P</option> <option value="cyanogen-bromide">cyanogen-bromide</option> <option value="Clostripain/P">Clostripain/P</option> <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> - <option value="no cleavage">no cleavage</option> - <option value="unspecific cleavage">unspecific cleavage</option> - <option value="Lys-C">Lys-C</option> - <option value="Lys-N">Lys-N</option> - <option value="Asp-N/B">Asp-N/B</option> - <option value="Asp-N_ambic">Asp-N_ambic</option> + <option value="V8-E">V8-E</option> + <option value="leukocyte elastase">leukocyte elastase</option> + <option value="proline endopeptidase">proline endopeptidase</option> + <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> <option value="Chymotrypsin">Chymotrypsin</option> <option value="Chymotrypsin/P">Chymotrypsin/P</option> <option value="CNBr">CNBr</option> + <option value="no cleavage">no cleavage</option> + <option value="unspecific cleavage">unspecific cleavage</option> <option value="Formic_acid">Formic_acid</option> + <option value="Lys-C">Lys-C</option> + <option value="Lys-N">Lys-N</option> + <option value="Asp-N">Asp-N</option> + <option value="Asp-N/B">Asp-N/B</option> + <option value="Asp-N_ambic">Asp-N_ambic</option> + <option value="Lys-C/P">Lys-C/P</option> + <option value="PepsinA">PepsinA</option> + <option value="Alpha-lytic protease">Alpha-lytic protease</option> + <option value="2-iodobenzoate">2-iodobenzoate</option> + <option value="iodosobenzoate">iodosobenzoate</option> + <option value="staphylococcal protease/D">staphylococcal protease/D</option> + <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> <option value="Arg-C">Arg-C</option> - <option value="V8-E">V8-E</option> - <option value="leukocyte elastase">leukocyte elastase</option> - <option value="proline endopeptidase">proline endopeptidase</option> + <option value="Arg-C/P">Arg-C/P</option> <expand macro="list_string_san"/> </param> </section> |
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| diff -r 7911914e96f6 -r 25cc460f9092 fill_ctd.py --- a/fill_ctd.py Wed Sep 09 19:56:16 2020 +0000 +++ b/fill_ctd.py Wed Sep 23 15:03:39 2020 +0000 |
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| @@ -150,6 +150,8 @@ # transform values from json that correspond to # - old style booleans (string + restrictions) -> transformed to a str +# - new style booleans that get a string (happens for hidden parameters [-test]) +# are transformed to a bool # - 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 @@ -164,7 +166,7 @@ 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 + # updated (better: then dash and the underscore variant are in the dict) # TODO might be removed later https://github.com/OpenMS/OpenMS/pull/4529 try: lineage = [_.replace("-", "_") for _ in p.get_lineage(name_only=True)] @@ -172,12 +174,16 @@ except KeyError: continue else: - setInDict(args, lineage, val) + setInDict(args, p.get_lineage(name_only=True), 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.type is bool: + v = getFromDict(args, p.get_lineage(name_only=True)) + if isinstance(v, str): + v = (v.lower() == "true") + setInDict(args, p.get_lineage(name_only=True), v) 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: |
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| diff -r 7911914e96f6 -r 25cc460f9092 generate.sh --- a/generate.sh Wed Sep 09 19:56:16 2020 +0000 +++ b/generate.sh Wed Sep 23 15:03:39 2020 +0000 |
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| @@ -67,6 +67,7 @@ patch PepNovoAdapter.xml < PepNovoAdapter.patch patch OMSSAAdapter.xml < OMSSAAdapter.patch +patch -p0 <404-urls.patch # #-b version log debug test in_type executable pepnovo_executable param_model_directory rt_concat_trafo_out param_id_pool |
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| diff -r 7911914e96f6 -r 25cc460f9092 hardcoded_params.json --- a/hardcoded_params.json Wed Sep 09 19:56:16 2020 +0000 +++ b/hardcoded_params.json Wed Sep 23 15:03:39 2020 +0000 |
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| @@ -164,7 +164,7 @@ "tools": ["PhosphoScoring"] }, { "CTD:type": "output-prefix", - "CTD:required": "true", + "CTD:required": true, "CTD:restrictions": "mzml", "tools": ["MzMLSplitter"] }, { @@ -234,13 +234,14 @@ "#": "output-prefix", "out_path": [{ "CTD:type": "output-prefix", - "CTD:required": "true", + "CTD:required": true, "CTD:restrictions": "idXML", "tools": ["IDRipper"] }], "outputDirectory": [{ "CTD:type": "output-prefix", - "CTD:required": "true", + "CTD:advanced": false, + "CTD:required": true, "CTD:restrictions": "mzml", "tools": ["OpenSwathFileSplitter"] }] |
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| diff -r 7911914e96f6 -r 25cc460f9092 macros_autotest.xml --- a/macros_autotest.xml Wed Sep 09 19:56:16 2020 +0000 +++ b/macros_autotest.xml Wed Sep 23 15:03:39 2020 +0000 |
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| @@ -1475,6 +1475,8 @@ </xml> <xml name="autotest_DeMeanderize"> </xml> + <xml name="autotest_Digestor"> +</xml> <xml name="autotest_DTAExtractor"> <test expect_num_outputs="1"> <conditional name="adv_opts_cond"> @@ -26315,4 +26317,4 @@ </output> </test> </xml> -<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> +<xml name="autotest_InspectAdapter"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_RTPredict"/><xml name="autotest_OpenSwathDIAPreScoring"/><xml name="autotest_DigestorMotif"/><xml name="autotest_PTPredict"/></macros> |
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| diff -r 7911914e96f6 -r 25cc460f9092 macros_discarded_auto.xml --- a/macros_discarded_auto.xml Wed Sep 09 19:56:16 2020 +0000 +++ b/macros_discarded_auto.xml Wed Sep 23 15:03:39 2020 +0000 |
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| @@ -7,7 +7,7 @@ <param name="test" value="true"/> </conditional> <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <output_collection name="adv_opts_cond.outputDirectory" count=""/> + <output_collection name="outputDirectory" count=""/> <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_qc_FLAG"/> <output name="ctd_out" ftype="xml"> |
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| diff -r 7911914e96f6 -r 25cc460f9092 macros_test.xml --- a/macros_test.xml Wed Sep 09 19:56:16 2020 +0000 +++ b/macros_test.xml Wed Sep 23 15:03:39 2020 +0000 |
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| @@ -293,7 +293,7 @@ </conditional> <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/> - <output_collection name="adv_opts_cond.outputDirectory" count="6"> + <output_collection name="outputDirectory" count="6"> <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/> <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/> </output_collection> |
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| diff -r 7911914e96f6 -r 25cc460f9092 test-data.sh --- a/test-data.sh Wed Sep 09 19:56:16 2020 +0000 +++ b/test-data.sh Wed Sep 23 15:03:39 2020 +0000 |
| [ |
| @@ -18,6 +18,11 @@ export OPENMSENV="$tmp/OpenMS$VERSION-env" export CTDCONVERTER="$tmp/CTDConverter" +if [[ -z "$1" ]]; then + autotests="/dev/null" +else + autotests="$1" +fi if type conda > /dev/null; then true @@ -28,11 +33,6 @@ fi eval "$(conda shell.bash hook)" -if [[ -z "$1" ]]; then - autotests="/dev/null" -else - autotests="$1" -fi ############################################################################### ## get @@ -88,7 +88,7 @@ git pull origin topic/cdata cd - fi -export PYTHONPATH=$(pwd)/CTDopts +# export PYTHONPATH=$(pwd)/CTDopts ############################################################################### ## copy all the test data files to test-data @@ -96,6 +96,8 @@ ## prepare_test_data ############################################################################### echo "Get test data" +find test-data -type f,l,d ! -name "*fa" ! -name "*loc" -delete + cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/ cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/ cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/ @@ -211,20 +213,17 @@ cd - || exit -# # # exit - ############################################################################### ## auto generate tests ############################################################################### - -echo "Write test macros to "$autotests -echo "<macros>" > $autotests +echo "Write test macros to $autotests" +echo "<macros>" > "$autotests" for i in $(ls *xml |grep -v macros) do b=$(basename "$i" .xml) - get_tests2 "$b" >> $autotests + get_tests2 "$b" >> "$autotests" done -echo "</macros>" >> $autotests +echo "</macros>" >> "$autotests" echo "Create test data links" link_tmp_files @@ -232,9 +231,16 @@ # tests for tools using output_prefix parameters can not be auto generated # hence we output the tests for manual curation in macros_test.xml # and remove them from the autotests +# -> OpenSwathFileSplitter IDRipper MzMLSplitter +# +# Furthermore we remove tests for tools without binaries in conda +# -> MSFragger MaRaClusterAdapter NovorAdapter +# +# not able to specify composite test data +# -> SpectraSTSearchAdapter if [[ ! -z "$1" ]]; then echo "" > macros_discarded_auto.xml - for i in OpenSwathFileSplitter IDRipper MzMLSplitter + for i in OpenSwathFileSplitter IDRipper MzMLSplitter MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter do echo "<xml name=\"manutest_$i\">" >> macros_discarded_auto.xml xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >> macros_discarded_auto.xml @@ -242,7 +248,7 @@ xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp mv tmp macros_autotest.xml done - >&2 "discarded autogenerated macros for curation in macros_discarded_auto.xml" + >&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml" fi conda deactivate |