Mercurial > repos > galaxyp > openms_featurefindermetaboident
diff test-data.sh @ 1:59c8b1a9cf86 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
author | galaxyp |
---|---|
date | Thu, 24 Sep 2020 12:21:43 +0000 |
parents | 539b683e9752 |
children | 7e29bf457263 |
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--- a/test-data.sh Wed Sep 09 19:59:38 2020 +0000 +++ b/test-data.sh Thu Sep 24 12:21:43 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