Mercurial > repos > galaxyp > openms_cometadapter
changeset 5:704cace078c4 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3cafa1cc1ea87eb7a0dc0e7aae013780c3565178"
author | galaxyp |
---|---|
date | Sat, 05 Dec 2020 19:51:29 +0000 |
parents | 1533239ed6f2 |
children | 75e0c261bd1a |
files | CometAdapter.xml bump.json generate.sh hardcoded_params.json macros.xml macros_autotest.xml macros_test.xml prepare_test_data_manual.sh readme.md |
diffstat | 9 files changed, 38 insertions(+), 24 deletions(-) [+] |
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--- a/CometAdapter.xml Fri Nov 06 19:19:46 2020 +0000 +++ b/CometAdapter.xml Sat Dec 05 19:51:29 2020 +0000 @@ -1,7 +1,7 @@ <?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> <!--Proposed Tool Section: [Identification]--> -<tool id="CometAdapter" name="CometAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="CometAdapter" name="CometAdapter" version="@TOOL_VERSION@+galaxy0" profile="20.05"> <description>Annotates MS/MS spectra using Comet.</description> <macros> <token name="@EXECUTABLE@">CometAdapter</token>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bump.json Sat Dec 05 19:51:29 2020 +0000 @@ -0,0 +1,9 @@ +{ +"AssayGeneratorMetabo": 1, +"LuciphorAdapter": 1, +"MSFraggerAdapter": 1, +"MSGFPlusAdapter": 1, +"NovorAdapter": 1, +"PSMFeatureExtractor": 1, +"SiriusAdapter": 1 +}
--- a/generate.sh Fri Nov 06 19:19:46 2020 +0000 +++ b/generate.sh Sat Dec 05 19:51:29 2020 +0000 @@ -6,8 +6,8 @@ ## FILETYPES_RE=$(grep -v "^#" $FILETYPES | grep -v "^$" | cut -f 1 -d" " | tr '\n' '|' | sed 's/|$//'| sed 's/|/\\|/g') export tmp=$(mktemp -d) + export CTDCONVERTER="$tmp/CTDConverter" - ############################################################################### ## reset old data ############################################################################### @@ -56,12 +56,14 @@ find . -maxdepth 0 -name "[A-Z]*xml" -delete source $(dirname $(which conda))/../etc/profile.d/conda.sh conda activate $tmp/OpenMS$VERSION-env -python $CTDCONVERTER/convert.py galaxy -i ctd/*ctd -o ./ -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p hardcoded_params.json --test-macros macros_autotest.xml --test-macros-prefix autotest_ --test-macros macros_test.xml --test-macros-prefix manutest_ --tool-version $VERSION --tool-profile $PROFILE > convert.out 2> convert.err +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 $PROFILE --bump-file bump.json > convert.out 2> convert.err if [[ "$?" -ne "0" ]]; then >&2 echo 'CTD -> XML conversion failed'; >&2 echo -e "stderr:\n$(cat convert.err)"; fi conda deactivate patch PepNovoAdapter.xml < PepNovoAdapter.patch patch OMSSAAdapter.xml < OMSSAAdapter.patch +# this should not be necessary from 2.7 https://github.com/OpenMS/OpenMS/pull/5087 +patch PSMFeatureExtractor.xml < PSMFeatureExtractor.patch # https://github.com/OpenMS/OpenMS/pull/4984 sed -i -e 's@http://www.openms.de/documentation/@http://www.openms.de/doxygen/release/2.6.0/html/@' ./*xml
--- a/hardcoded_params.json Fri Nov 06 19:19:46 2020 +0000 +++ b/hardcoded_params.json Sat Dec 05 19:51:29 2020 +0000 @@ -122,6 +122,9 @@ "sirius:cores": [{ "value": "${GALAXY_SLOTS:-1}" }], + "out_workspace_directory": [{ + "value": "__SIRIUS_WORKSPACE__" + }], "#": "hardcode the outer loop threads for OpenSwathWorkflow", "outer_loop_threads": [{
--- a/macros.xml Fri Nov 06 19:19:46 2020 +0000 +++ b/macros.xml Sat Dec 05 19:51:29 2020 +0000 @@ -4,7 +4,6 @@ add additional macro files using the m/macros parameter --> <macros> <token name="@TOOL_VERSION@">2.6</token> - <token name="@GALAXY_VERSION@">0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">openms</requirement> @@ -21,6 +20,7 @@ <xml name="stdio"> <stdio> <regex match="std::bad_alloc" level="fatal_oom" description="Could not allocate memory"/> + <regex match="OutOfMemoryError" level="fatal_oom" description="Could not allocate memory"/> <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/> <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/> <regex match="qUncompress: could not allocate enough memory to uncompress data" level="fatal_oom" description="Java memory Exception"/>
--- a/macros_autotest.xml Fri Nov 06 19:19:46 2020 +0000 +++ b/macros_autotest.xml Sat Dec 05 19:51:29 2020 +0000 @@ -126,7 +126,6 @@ <param name="max_transitions" value="3"/> <param name="cosine_similarity_threshold" value="0.98"/> <param name="transition_threshold" value="5.0"/> - <param name="out_workspace_directory" value=""/> <section name="deisotoping"> <param name="use_deisotoper" value="false"/> <param name="fragment_tolerance" value="1.0"/> @@ -195,7 +194,6 @@ <param name="max_transitions" value="3"/> <param name="cosine_similarity_threshold" value="0.98"/> <param name="transition_threshold" value="5.0"/> - <param name="out_workspace_directory" value=""/> <section name="deisotoping"> <param name="use_deisotoper" value="false"/> <param name="fragment_tolerance" value="1.0"/> @@ -264,7 +262,6 @@ <param name="max_transitions" value="3"/> <param name="cosine_similarity_threshold" value="0.98"/> <param name="transition_threshold" value="5.0"/> - <param name="out_workspace_directory" value=""/> <section name="deisotoping"> <param name="use_deisotoper" value="false"/> <param name="fragment_tolerance" value="1.0"/> @@ -333,7 +330,6 @@ <param name="max_transitions" value="3"/> <param name="cosine_similarity_threshold" value="0.98"/> <param name="transition_threshold" value="5.0"/> - <param name="out_workspace_directory" value=""/> <section name="deisotoping"> <param name="use_deisotoper" value="false"/> <param name="fragment_tolerance" value="1.0"/> @@ -402,7 +398,6 @@ <param name="max_transitions" value="3"/> <param name="cosine_similarity_threshold" value="0.98"/> <param name="transition_threshold" value="5.0"/> - <param name="out_workspace_directory" value=""/> <section name="deisotoping"> <param name="use_deisotoper" value="false"/> <param name="fragment_tolerance" value="1.0"/> @@ -471,7 +466,6 @@ <param name="max_transitions" value="3"/> <param name="cosine_similarity_threshold" value="0.98"/> <param name="transition_threshold" value="3.0"/> - <param name="out_workspace_directory" value=""/> <section name="deisotoping"> <param name="use_deisotoper" value="false"/> <param name="fragment_tolerance" value="1.0"/> @@ -540,7 +534,6 @@ <param name="max_transitions" value="3"/> <param name="cosine_similarity_threshold" value="0.98"/> <param name="transition_threshold" value="3.0"/> - <param name="out_workspace_directory" value=""/> <section name="deisotoping"> <param name="use_deisotoper" value="false"/> <param name="fragment_tolerance" value="1.0"/> @@ -609,7 +602,6 @@ <param name="max_transitions" value="3"/> <param name="cosine_similarity_threshold" value="0.98"/> <param name="transition_threshold" value="3.0"/> - <param name="out_workspace_directory" value=""/> <section name="deisotoping"> <param name="use_deisotoper" value="false"/> <param name="fragment_tolerance" value="1.0"/> @@ -678,7 +670,6 @@ <param name="max_transitions" value="3"/> <param name="cosine_similarity_threshold" value="0.98"/> <param name="transition_threshold" value="3.0"/> - <param name="out_workspace_directory" value=""/> <section name="deisotoping"> <param name="use_deisotoper" value="false"/> <param name="fragment_tolerance" value="1.0"/> @@ -24819,6 +24810,8 @@ </output> </test> </xml> + <xml name="autotest_PSMFeatureExtractor_org"> +</xml> <xml name="autotest_PSMFeatureExtractor"> </xml> <xml name="autotest_PTModel"> @@ -25472,7 +25465,6 @@ </conditional> <param name="in" value="SiriusAdapter_1_input.mzML"/> <output name="out_sirius" file="SiriusAdapter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="out_workspace_directory" value=""/> <section name="preprocessing"> <param name="filter_by_num_masstraces" value="1"/> <param name="precursor_mz_tolerance" value="0.005"/> @@ -25515,7 +25507,6 @@ <param name="in" value="SiriusAdapter_2_input.mzML"/> <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/> <output name="out_sirius" file="SiriusAdapter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="out_workspace_directory" value=""/> <section name="preprocessing"> <param name="filter_by_num_masstraces" value="3"/> <param name="precursor_mz_tolerance" value="0.005"/> @@ -25558,7 +25549,6 @@ <param name="in" value="SiriusAdapter_3_input.mzML"/> <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/> <output name="out_sirius" file="SiriusAdapter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="out_workspace_directory" value=""/> <section name="preprocessing"> <param name="filter_by_num_masstraces" value="3"/> <param name="precursor_mz_tolerance" value="0.005"/> @@ -25601,7 +25591,6 @@ <param name="in" value="SiriusAdapter_3_input.mzML"/> <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/> <output name="out_ms" file="SiriusAdapter_5_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/> - <param name="out_workspace_directory" value=""/> <section name="preprocessing"> <param name="filter_by_num_masstraces" value="1"/> <param name="precursor_mz_tolerance" value="0.005"/> @@ -25644,7 +25633,6 @@ <param name="in" value="SiriusAdapter_4_input.mzML"/> <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/> <output name="out_ms" file="SiriusAdapter_6_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/> - <param name="out_workspace_directory" value=""/> <section name="preprocessing"> <param name="filter_by_num_masstraces" value="1"/> <param name="precursor_mz_tolerance" value="0.005"/> @@ -25687,7 +25675,6 @@ <param name="in" value="SiriusAdapter_4_input.mzML"/> <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/> <output name="out_sirius" file="SiriusAdapter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="out_workspace_directory" value=""/> <section name="preprocessing"> <param name="filter_by_num_masstraces" value="1"/> <param name="precursor_mz_tolerance" value="0.005"/> @@ -25731,7 +25718,6 @@ <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/> <output name="out_sirius" file="SiriusAdapter_4_output.tmp" compare="sim_size" delta="5700" ftype="mztab"/> <output name="out_fingerid" file="SiriusAdapter_4_foutput.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="out_workspace_directory" value=""/> <section name="preprocessing"> <param name="filter_by_num_masstraces" value="1"/> <param name="precursor_mz_tolerance" value="0.005"/> @@ -27202,4 +27188,4 @@ </output> </test> </xml> -<xml name="autotest_PTPredict"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_RTPredict"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_InspectAdapter"/></macros> +<xml name="autotest_RTPredict"/><xml name="autotest_InspectAdapter"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_PTPredict"/></macros>
--- a/macros_test.xml Fri Nov 06 19:19:46 2020 +0000 +++ b/macros_test.xml Sat Dec 05 19:51:29 2020 +0000 @@ -335,6 +335,7 @@ <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/> </test> </xml> +<!-- TODO PSMFeatureExtractor should have auto tests with 2.7 https://github.com/OpenMS/OpenMS/pull/5087 --> <xml name="manutest_PSMFeatureExtractor"> <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible --> <param name="adv_opts_cond|test" value="true"/> @@ -354,6 +355,13 @@ <param name="out_type" value="mzid"/> <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="500"/> </test> + <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible --> + <param name="adv_opts_cond|test" value="true"/> + <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/> + <param name="adv_opts_cond|adv_opts_selector" value="advanced"/> + <param name="out_type" value="idxml"/> + <output name="out" ftype="idxml" value="PSMFeatureExtractor_3.idXML" compare="sim_size" delta="500"/> + </test> </xml> <xml name="manutest_QCCalculator"> <test expect_num_outputs="1"><!-- took test data from another test w mzML input -->
--- a/prepare_test_data_manual.sh Fri Nov 06 19:19:46 2020 +0000 +++ b/prepare_test_data_manual.sh Sat Dec 05 19:51:29 2020 +0000 @@ -86,10 +86,13 @@ PhosphoScoring -in spectra.mzML -id MSGFPlusAdapter_1_out1.tmp -out PhosphoScoring.idxml > PhosphoScoring.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out PSMFeatureExtractor.idxml > PSMFeatureExtractor_1.stdout 2> stderr +# TODO PSMFeatureExtractor should have auto tests with 2.7 https://github.com/OpenMS/OpenMS/pull/5087 +PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out_type idXML -out PSMFeatureExtractor.idxml > PSMFeatureExtractor_1.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out PSMFeatureExtractor.mzid > PSMFeatureExtractor_2.stdout 2> stderr +PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out_type mzid -out PSMFeatureExtractor.mzid > PSMFeatureExtractor_2.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi +PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML -out_type idXML -out PSMFeatureExtractor_3.idXML > PSMFeatureExtractor_3.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_3 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi QCCalculator -test -in OpenPepXL_input.mzML -out QCCalculator1.qcML > QCCalculator_1.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'QCCalculator_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi
--- a/readme.md Fri Nov 06 19:19:46 2020 +0000 +++ b/readme.md Sat Dec 05 19:51:29 2020 +0000 @@ -22,11 +22,14 @@ Manual updates should only be done to -- the `@GALAXY_VERSION@"` token in `macros.xml` - and the manually contributed tests in `macros_test.xml` (The goal is that all tools that do not have an automatically generated test are covered here) - the `hardcoded_params.json` files +Wrapper versions are managed in `bump.json`. For tools listed in the file +the wrapper version will be set accordingly and otherwise `0` is used. +For a major update of the tool version the bump file should be reset (to `{}`). + In a few cases patches may be acceptable. Installation