diff --git a/.github/workflows/framework.yaml b/.github/workflows/framework.yaml new file mode 100644 index 000000000000..55aa99f62198 --- /dev/null +++ b/.github/workflows/framework.yaml @@ -0,0 +1,40 @@ +name: Framework tests +on: [push, pull_request] +env: + GALAXY_TEST_DBURI: 'postgres://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8' +jobs: + test: + name: Test + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ['3.7'] + services: + postgres: + image: postgres:11 + env: + POSTGRES_USER: postgres + POSTGRES_PASSWORD: postgres + POSTGRES_DB: postgres + ports: + - 5432:5432 + steps: + - uses: actions/checkout@v2 + with: + path: 'galaxy root' + - uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python-version }} + - name: Cache pip dir + uses: actions/cache@v2 + with: + path: ~/.cache/pip + key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }} + - name: Run tests + run: ./run_tests.sh --framework + working-directory: 'galaxy root' + - uses: actions/upload-artifact@v2 + if: failure() + with: + name: Framework test results (${{ matrix.python-version }}) + path: 'galaxy root/run_framework_tests.html' diff --git a/lib/galaxy_test/api/test_tools_upload.py b/lib/galaxy_test/api/test_tools_upload.py index 5a4c443428ee..af035505f090 100644 --- a/lib/galaxy_test/api/test_tools_upload.py +++ b/lib/galaxy_test/api/test_tools_upload.py @@ -1,5 +1,7 @@ import json +import pytest + from galaxy.tool_util.verify.test_data import TestDataResolver from galaxy_test.base.constants import ( ONE_TO_SIX_ON_WINDOWS, @@ -754,8 +756,12 @@ def test_upload_force_composite(self): assert extra_file["path"] == "composite" assert extra_file["class"] == "File" - @skip_if_site_down("https://usegalaxy.org") def test_upload_from_invalid_url(self): + with pytest.raises(AssertionError): + self._upload('https://foo.invalid', assert_ok=False) + + @skip_if_site_down("https://usegalaxy.org") + def test_upload_from_404_url(self): history_id, new_dataset = self._upload('https://usegalaxy.org/bla123', assert_ok=False) dataset_details = self.dataset_populator.get_history_dataset_details(history_id, dataset_id=new_dataset["id"], assert_ok=False) assert dataset_details['state'] == 'error', "expected dataset state to be 'error', but got '%s'" % dataset_details['state'] diff --git a/lib/galaxy_test/base/populators.py b/lib/galaxy_test/base/populators.py index 404edb28c349..b3dba9338a20 100644 --- a/lib/galaxy_test/base/populators.py +++ b/lib/galaxy_test/base/populators.py @@ -111,19 +111,20 @@ def wrapped_method(api_test_case, *args, **kwargs): return method_wrapper -def skip_if_site_down(url): +def is_site_up(url): + try: + response = requests.get(url, timeout=10) + return response.status_code == 200 + except Exception: + return False - def site_down(): - try: - response = requests.get(url, timeout=10) - return response.status_code != 200 - except Exception: - return False + +def skip_if_site_down(url): def method_wrapper(method): @wraps(method) def wrapped_method(api_test_case, *args, **kwargs): - _raise_skip_if(site_down(), "Test depends on [%s] being up and it appears to be down." % url) + _raise_skip_if(not is_site_up(url), f"Test depends on [{url}] being up and it appears to be down.") method(api_test_case, *args, **kwargs) return wrapped_method diff --git a/lib/galaxy_test/selenium/test_workflow_editor.py b/lib/galaxy_test/selenium/test_workflow_editor.py index d410d98b3efe..b7b9247bcdf9 100644 --- a/lib/galaxy_test/selenium/test_workflow_editor.py +++ b/lib/galaxy_test/selenium/test_workflow_editor.py @@ -198,7 +198,7 @@ def test_non_data_connections(self): # Also the connector should disappear tool_input.wait_for_absent_or_hidden() - # Now make it connected again and watch the requestss + # Now make it connected again and watch the requests connect_icon.wait_for_and_click() tool_input.wait_for_visible() diff --git a/test/functional/tools/bibtex.xml b/test/functional/tools/bibtex.xml index 113a07b44ced..a3b3bd4986ae 100644 --- a/test/functional/tools/bibtex.xml +++ b/test/functional/tools/bibtex.xml @@ -10,10 +10,10 @@ name="Galaxy IUC" /> - Citation.js + Citation.js "$out_file1" +echo '$input1' > '$out_file1' ]]> @@ -21,17 +21,18 @@ - - + + + + ]]> - 10.1101/gr.4086505 - 10.6084/m9.figshare.979190 - + 10.1101/gr.4086505 + 10.6084/m9.figshare.979190 + @misc{Garrison2015, author = {Garrison, Erik}, year = {2015}, @@ -40,8 +41,8 @@ journal = {GitHub repository}, url = {https://github.com/ekg/vcflib}, } - - + + @online{lh32017, author = {Heng Li}, year = {2017}, @@ -50,19 +51,19 @@ journal = {GitHub repository}, url = {https://github.com/lh3/bwa}, } - - - + + + @ARTICLE{article-minimal, author = {L[eslie] A. Aamport}, title = {The Gnats and Gnus Document Preparation System}, journal = {\mbox{G-Animal's} Journal}, year = 1986, } - - + + @ARTICLE{article-full, author = {L[eslie] A. Aamport}, title = {The Gnats and Gnus Document Preparation System}, @@ -74,8 +75,8 @@ month = jul, note = "This is a full ARTICLE entry", } - - + + @INBOOK{inbook-minimal, author = "Donald E. Knuth", title = "Fundamental Algorithms", @@ -83,8 +84,9 @@ year = "{\noopsort{1973b}}1973", chapter = "1.2", -} - +} + + @INBOOK{inbook-full, author = "Donald E. Knuth", title = "Fundamental Algorithms", @@ -100,16 +102,16 @@ pages = "10--119", note = "This is a full INBOOK entry", } - - + + @BOOK{book-minimal, author = "Donald E. Knuth", title = "Seminumerical Algorithms", publisher = "Addison-Wesley", year = "{\noopsort{1973c}}1981", } - - + + @BOOK{book-full, author = "Donald E. Knuth", title = "Seminumerical Algorithms", @@ -122,8 +124,8 @@ year = "{\noopsort{1973c}}1981", note = "This is a full BOOK entry", } - - + + @BOOK{whole-set, author = "Donald E. Knuth", publisher = "Addison-Wesley", @@ -132,8 +134,8 @@ year = "{\noopsort{1973a}}{\switchargs{--90}{1968}}", note = "Seven volumes planned (this is a cross-referenced set of BOOKs)", } - - + + @BOOKLET{booklet-full, author = "Jill C. Knvth", title = "The Programming of Computer Art", @@ -143,8 +145,8 @@ year = 1988, note = "This is a full BOOKLET entry", } - - + + @INCOLLECTION{incollection-minimal, author = "Daniel D. Lincoll", title = "Semigroups of Recurrences", @@ -152,8 +154,8 @@ publisher = "Academic Press", year = 1977, } - - + + @INCOLLECTION{incollection-full, author = "Daniel D. Lincoll", title = "Semigroups of Recurrences", @@ -171,8 +173,8 @@ year = 1977, note = "This is a full INCOLLECTION entry", } - - + + @BOOK{whole-collection, editor = "David J. Lipcoll and D. H. Lawrie and A. H. Sameh", title = "High Speed Computer and Algorithm Organization", @@ -185,8 +187,8 @@ month = sep, year = 1977, } - - + + @MANUAL{manual-full, author = "Larry Manmaker", title = "The Definitive Computer Manual", @@ -197,16 +199,16 @@ year = 1986, note = "This is a full MANUAL entry", } - - + + @MASTERSTHESIS{mastersthesis-minimal, author = "{\'{E}}douard Masterly", title = "Mastering Thesis Writing", school = "Stanford University", year = 1988, } - - + + @MASTERSTHESIS{mastersthesis-full, author = "{\'{E}}douard Masterly", title = "Mastering Thesis Writing", @@ -217,8 +219,8 @@ year = 1988, note = "This is a full MASTERSTHESIS entry", } - - + + @MISC{misc-full, author = "Joe-Bob Missilany", title = "Handing out random pamphlets in airports", @@ -227,16 +229,16 @@ year = 1984, note = "This is a full MISC entry", } - - + + @INPROCEEDINGS{inproceedings-minimal, author = "Alfred V. Oaho and Jeffrey D. Ullman and Mihalis Yannakakis", title = "On Notions of Information Transfer in {VLSI} Circuits", booktitle = "Proc. Fifteenth Annual ACM" # STOC, year = 1983, } - - + + @INPROCEEDINGS{inproceedings-full, author = "Alfred V. Oaho and Jeffrey D. Ullman and Mihalis Yannakakis", title = "On Notions of Information Transfer in {VLSI} Circuits", @@ -252,8 +254,8 @@ publisher = "Academic Press", note = "This is a full INPROCEDINGS entry", } - - + + @INPROCEEDINGS{inproceedings-crossref, crossref = "whole-proceedings", author = "Alfred V. Oaho and Jeffrey D. Ullman and Mihalis Yannakakis", @@ -262,8 +264,8 @@ pages = "133--139", note = "This is a cross-referencing INPROCEEDINGS entry", } - - + + @PROCEEDINGS{proceedings-full, editor = "Wizard V. Oz and Mihalis Yannakakis", title = "Proc. Fifteenth Annual" # STOC, @@ -276,16 +278,16 @@ publisher = "Academic Press", note = "This is a full PROCEEDINGS entry", } - - + + @PHDTHESIS{phdthesis-minimal, author = "F. Phidias Phony-Baloney", title = "Fighting Fire with Fire: Festooning {F}rench Phrases", school = "Fanstord University", year = 1988, } - - + + @PHDTHESIS{phdthesis-full, author = "F. Phidias Phony-Baloney", title = "Fighting Fire with Fire: Festooning {F}rench Phrases", @@ -296,16 +298,16 @@ year = 1988, note = "This is a full PHDTHESIS entry", } - - + + @TECHREPORT{techreport-minimal, author = "Tom Terrific", title = "An {$O(n \log n / \! \log\log n)$} Sorting Algorithm", institution = "Fanstord University", year = 1988, } - - + + @TECHREPORT{techreport-full, author = "Tom T{\'{e}}rrific", title = "An {$O(n \log n / \! \log\log n)$} Sorting Algorithm", @@ -317,15 +319,15 @@ year = 1988, note = "This is a full TECHREPORT entry", } - - + + @UNPUBLISHED{unpublished-minimal, author = "Ulrich {\"{U}}nderwood and Ned {\~N}et and Paul {\={P}}ot", title = "Lower Bounds for Wishful Research Results", note = "Talk at Fanstord University (this is a minimal UNPUBLISHED entry)", } - - + + @UNPUBLISHED{unpublished-full, author = "Ulrich {\"{U}}nderwood and Ned {\~N}et and Paul {\={P}}ot", title = "Lower Bounds for Wishful Research Results", @@ -333,6 +335,6 @@ year = 1988, note = "Talk at Fanstord University (this is a full UNPUBLISHED entry)", } - + diff --git a/test/functional/tools/catDocker.xml b/test/functional/tools/catDocker.xml index 470fef9ccf09..5cef7257ca16 100644 --- a/test/functional/tools/catDocker.xml +++ b/test/functional/tools/catDocker.xml @@ -1,18 +1,17 @@ - + tail-to-head - busybox:ubuntu-14.04 + busybox:ubuntu-14.04 - - echo "Galaxy slots passed through contain as \$GALAXY_SLOTS"; - cat $input1 - #for $q in $queries - ${q.input2} - #end for - > $out_file1; - echo "Work dir output" > working_file - - + '$out_file1' && +echo 'Work dir output' > working_file + ]]> @@ -23,6 +22,8 @@ + + diff --git a/test/functional/tools/collection_cat_group_tag.xml b/test/functional/tools/collection_cat_group_tag.xml index cdda1b94e917..3e0ac6c7ef57 100644 --- a/test/functional/tools/collection_cat_group_tag.xml +++ b/test/functional/tools/collection_cat_group_tag.xml @@ -1,12 +1,12 @@ - + tail-to-head - - cat - #for $file in $input1.get_datasets_for_group($group): - '$file' - #end for - > '$out_file1' - + '$out_file1' + ]]> diff --git a/test/functional/tools/collection_cat_group_tag_multiple.xml b/test/functional/tools/collection_cat_group_tag_multiple.xml index c534f17258ef..e97d58843788 100644 --- a/test/functional/tools/collection_cat_group_tag_multiple.xml +++ b/test/functional/tools/collection_cat_group_tag_multiple.xml @@ -1,13 +1,13 @@ - + tail-to-head - cat - #for $group in $groups: - #for $file in $input1.get_datasets_for_group($group): - '$file' - #end for - #end for - > '$out_file1' +cat +#for $group in $groups: + #for $file in $input1.get_datasets_for_group($group): + '$file' + #end for +#end for +> '$out_file1' diff --git a/test/functional/tools/column_multi_param.xml b/test/functional/tools/column_multi_param.xml index 4d220372f408..5f4b899e42bc 100644 --- a/test/functional/tools/column_multi_param.xml +++ b/test/functional/tools/column_multi_param.xml @@ -1,25 +1,25 @@ - - - #for $input in $input1# - cut -f '$col' '$input' >> 'col_output'; - #end for# - - - - - - - - - - - - - - - - - - - + + > 'col_output'; +#end for# + ]]> + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/column_param.xml b/test/functional/tools/column_param.xml index 8da1374745e4..e62b33a2e31f 100644 --- a/test/functional/tools/column_param.xml +++ b/test/functional/tools/column_param.xml @@ -1,50 +1,50 @@ - - + '$output1' && echo "col $col" > '$output2' && echo "col_names $col_names" >> '$output2' - ]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/column_param_configfile.xml b/test/functional/tools/column_param_configfile.xml index 203afb44b705..6aa1b71d594d 100644 --- a/test/functional/tools/column_param_configfile.xml +++ b/test/functional/tools/column_param_configfile.xml @@ -1,10 +1,10 @@ - - - - - + + + + - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/composite.xml b/test/functional/tools/composite.xml index f4c5e5bfc1b0..7b2cd72eecce 100644 --- a/test/functional/tools/composite.xml +++ b/test/functional/tools/composite.xml @@ -1,20 +1,21 @@ - cat '$input.extra_files_path/Sequences' > $output - - - - - - - - - - - - - - - - - + '$output' + ]]> + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/composite_output.xml b/test/functional/tools/composite_output.xml index cc29995c1e3d..9e5f574809d5 100644 --- a/test/functional/tools/composite_output.xml +++ b/test/functional/tools/composite_output.xml @@ -1,26 +1,31 @@ - mkdir $output.extra_files_path; cp $input.extra_files_path/* $output.extra_files_path; cp $input.extra_files_path/Log $output.extra_files_path/second_log; mkdir $output.extra_files_path/nested; cp $input.extra_files_path/Log $output.extra_files_path/nested/nested_log - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/create_10.xml b/test/functional/tools/create_10.xml index e459b13ec031..bb7d2a288de7 100644 --- a/test/functional/tools/create_10.xml +++ b/test/functional/tools/create_10.xml @@ -1,16 +1,16 @@ - + create 10 datasets for testing tools with many outputs 1; - echo "2" > 2; - echo "3" > 3; - echo "4" > 4; - echo "5" > 5; - echo "6" > 6; - echo "7" > 7; - echo "8" > 8; - echo "9" > 9; - echo "10" > 10; +echo '1' > 1 && +echo '2' > 2 && +echo '3' > 3 && +echo '4' > 4 && +echo '5' > 5 && +echo '6' > 6 && +echo '7' > 7 && +echo '8' > 8 && +echo '9' > 9 && +echo '10' > 10 ]]> diff --git a/test/functional/tools/create_2.xml b/test/functional/tools/create_2.xml index f04bab7f4a9f..0cebbd6f8a59 100644 --- a/test/functional/tools/create_2.xml +++ b/test/functional/tools/create_2.xml @@ -1,11 +1,11 @@ - + '$out_file1'; - echo "2" > '$out_file2'; - sleep '$sleep_time'; +echo '1' > '$out_file1' && +echo '2' > '$out_file2' && +sleep $sleep_time ]]> - + diff --git a/test/functional/tools/dbkey_filter_input.xml b/test/functional/tools/dbkey_filter_input.xml index 534d07087b99..ae04f6fc58f5 100644 --- a/test/functional/tools/dbkey_filter_input.xml +++ b/test/functional/tools/dbkey_filter_input.xml @@ -1,20 +1,20 @@ Filter (single) input on a dbkey - - cat $inputs > $output - + '$output' + ]]> - + - - - - + + + + - + @@ -37,7 +37,6 @@ - diff --git a/test/functional/tools/dbkey_filter_multi_input.xml b/test/functional/tools/dbkey_filter_multi_input.xml index 5564b85eb5fa..df04926938dd 100644 --- a/test/functional/tools/dbkey_filter_multi_input.xml +++ b/test/functional/tools/dbkey_filter_multi_input.xml @@ -1,23 +1,22 @@ Filter select on dbkey of multiple inputs and use of named column > $output; - #end for# - ]]> - +#for $input in $inputs# + cat '$input' >> '$output'; +#end for# + ]]> - + - - - - + + + + - + @@ -40,7 +39,6 @@ - diff --git a/test/functional/tools/dbkey_output_action.xml b/test/functional/tools/dbkey_output_action.xml index 9d100105ec5c..128e43d721fa 100644 --- a/test/functional/tools/dbkey_output_action.xml +++ b/test/functional/tools/dbkey_output_action.xml @@ -1,16 +1,18 @@ - echo foo > $mapped_reads + '$mapped_reads' + ]]> - - - - + + + + - + \ No newline at end of file + diff --git a/test/functional/tools/detect_errors.xml b/test/functional/tools/detect_errors.xml index 724c5f7f8e8e..69cee555feeb 100644 --- a/test/functional/tools/detect_errors.xml +++ b/test/functional/tools/detect_errors.xml @@ -11,13 +11,13 @@ 2& echo "$stderrmsg"; - #end if - sh -c "exit $exit_code" +#if str($stdoutmsg) != "" + echo '$stdoutmsg' && +#end if +#if str($stderrmsg) != "" + >2& echo '$stderrmsg' && +#end if +sh -c 'exit $exit_code' ]]> diff --git a/test/functional/tools/disambiguate_cond.xml b/test/functional/tools/disambiguate_cond.xml index a85e91ce7c04..80e0b28326ce 100644 --- a/test/functional/tools/disambiguate_cond.xml +++ b/test/functional/tools/disambiguate_cond.xml @@ -1,47 +1,47 @@ - - - echo "$p1.p1v $p2.p2v $p3.p3v" > $out_file1; - #if $files.attach_files - cat "$files.p4.file" >> $out_file1; - #else - echo "no file specified" >> $out_file1; - #end if - + + '$out_file1' && +#if $files.attach_files + cat '$files.p4.file' >> '$out_file1' +#else + echo 'no file specified' >> '$out_file1' +#end if + ]]> - + - + - + - + - + - + - + - + - + - + - + diff --git a/test/functional/tools/disambiguate_repeats.xml b/test/functional/tools/disambiguate_repeats.xml index 7537a1f1e8c1..c20e72dcc290 100644 --- a/test/functional/tools/disambiguate_repeats.xml +++ b/test/functional/tools/disambiguate_repeats.xml @@ -1,6 +1,6 @@ - + - cat #for $q in $queries# ${q.input} #end for# #for $q in $more_queries# ${q.input} #end for# > $out_file1 +cat #for $q in $queries# '${q.input}' #end for# #for $q in $more_queries# '${q.input}' #end for# > '$out_file1' @@ -58,6 +58,5 @@ - diff --git a/test/functional/tools/exit_code_from_env.xml b/test/functional/tools/exit_code_from_env.xml index 970a7272e48a..1c5dc300b110 100644 --- a/test/functional/tools/exit_code_from_env.xml +++ b/test/functional/tools/exit_code_from_env.xml @@ -1,9 +1,9 @@ - + '$out_file1'; - : \${GX_TARGET_EXIT_CODE:-0}; - exit \${GX_TARGET_EXIT_CODE}; +echo 'Hello' > '$out_file1' && +: \${GX_TARGET_EXIT_CODE:-0} && +exit \${GX_TARGET_EXIT_CODE} ]]> @@ -11,8 +11,6 @@ - - @@ -23,4 +21,6 @@ + + diff --git a/test/functional/tools/exit_code_from_file.xml b/test/functional/tools/exit_code_from_file.xml index 5d66d96aa3ca..309227412c1c 100644 --- a/test/functional/tools/exit_code_from_file.xml +++ b/test/functional/tools/exit_code_from_file.xml @@ -1,6 +1,6 @@ - + - sh -c "exit `cat $input`" +sh -c "exit \$(cat '$input')" @@ -8,6 +8,8 @@ + + diff --git a/test/functional/tools/exit_code_oom.xml b/test/functional/tools/exit_code_oom.xml index ee9296570d91..e4e2b0cc86bd 100644 --- a/test/functional/tools/exit_code_oom.xml +++ b/test/functional/tools/exit_code_oom.xml @@ -1,16 +1,15 @@ @@ -22,8 +21,6 @@ - - @@ -34,4 +31,6 @@ + + diff --git a/test/functional/tools/expression_forty_two.xml b/test/functional/tools/expression_forty_two.xml index af6afd0d997a..6146b7fb9608 100644 --- a/test/functional/tools/expression_forty_two.xml +++ b/test/functional/tools/expression_forty_two.xml @@ -11,5 +11,9 @@ - Produces the integer 42. + + + diff --git a/test/functional/tools/expression_log_line_count.xml b/test/functional/tools/expression_log_line_count.xml index b58117699063..321837860711 100644 --- a/test/functional/tools/expression_log_line_count.xml +++ b/test/functional/tools/expression_log_line_count.xml @@ -10,5 +10,8 @@ - + + + + diff --git a/test/functional/tools/expression_parse_int.xml b/test/functional/tools/expression_parse_int.xml index 3e2080aac0c0..acf41fa54c01 100644 --- a/test/functional/tools/expression_parse_int.xml +++ b/test/functional/tools/expression_parse_int.xml @@ -10,5 +10,9 @@ - Parse an integer from text. + + + diff --git a/test/functional/tools/expression_pick_larger_file.xml b/test/functional/tools/expression_pick_larger_file.xml index eca011bb213e..3aef4bdf04e9 100644 --- a/test/functional/tools/expression_pick_larger_file.xml +++ b/test/functional/tools/expression_pick_larger_file.xml @@ -16,14 +16,12 @@ } ]]> - - + + - + - - @@ -41,4 +39,6 @@ + + diff --git a/test/functional/tools/fail_identifier.xml b/test/functional/tools/fail_identifier.xml index c9f4aac2aa44..5f9fa65865e9 100644 --- a/test/functional/tools/fail_identifier.xml +++ b/test/functional/tools/fail_identifier.xml @@ -1,10 +1,13 @@ - + + + + @@ -13,9 +16,8 @@ - - - + + diff --git a/test/functional/tools/fail_writing_work_dir_file.xml b/test/functional/tools/fail_writing_work_dir_file.xml index fe3005a764d1..d360fd709352 100644 --- a/test/functional/tools/fail_writing_work_dir_file.xml +++ b/test/functional/tools/fail_writing_work_dir_file.xml @@ -1,9 +1,9 @@ 'foo.txt' - #end if +echo 'Some output' && +#if not $failbool + echo 'Hello World' > 'foo.txt' +#end if ]]> @@ -11,6 +11,8 @@ + + diff --git a/test/functional/tools/filter_static_regexp.xml b/test/functional/tools/filter_static_regexp.xml index 367a16f2484c..ebfcd0756e81 100644 --- a/test/functional/tools/filter_static_regexp.xml +++ b/test/functional/tools/filter_static_regexp.xml @@ -1,45 +1,45 @@ Filter by static value and regexp - - echo $index_static > '$output' - echo $index_static_keep >> '$output' - echo $index_regexp >> '$output' - echo $index_regexp_keep >> '$output' - + '$output' && +echo $index_static_keep >> '$output' && +echo $index_regexp >> '$output' && +echo $index_regexp_keep >> '$output' && + ]]> - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - + @@ -88,7 +88,6 @@ - diff --git a/test/functional/tools/for_workflows/cat.xml b/test/functional/tools/for_workflows/cat.xml index 850469141fdc..952842a5d580 100644 --- a/test/functional/tools/for_workflows/cat.xml +++ b/test/functional/tools/for_workflows/cat.xml @@ -1,8 +1,8 @@ - + tail-to-head - - cat $input1 #for $q in $queries# ${q.input2} #end for# > $out_file1 - + '$out_file1' + ]]> diff --git a/test/functional/tools/for_workflows/cat_collection.xml b/test/functional/tools/for_workflows/cat_collection.xml index ff1f54f645b6..13ba958a47b1 100644 --- a/test/functional/tools/for_workflows/cat_collection.xml +++ b/test/functional/tools/for_workflows/cat_collection.xml @@ -1,10 +1,10 @@ - + tail-to-head cat #for $q in $input1# '$q' #end for# >'$out_file1' - + diff --git a/test/functional/tools/for_workflows/cat_interleave.xml b/test/functional/tools/for_workflows/cat_interleave.xml index 61d8d1a5efed..e5918a1f341b 100644 --- a/test/functional/tools/for_workflows/cat_interleave.xml +++ b/test/functional/tools/for_workflows/cat_interleave.xml @@ -1,8 +1,8 @@ - - - cat $input1 $input2 > $out_file1; - cat $input2 $input1 > $out_file2; - + + '$out_file1' && +cat '$input2' '$input1' > '$out_file2' + ]]> diff --git a/test/functional/tools/for_workflows/cat_list.xml b/test/functional/tools/for_workflows/cat_list.xml index fd761b74888e..1ba335f6dfd1 100644 --- a/test/functional/tools/for_workflows/cat_list.xml +++ b/test/functional/tools/for_workflows/cat_list.xml @@ -1,10 +1,10 @@ - - tail-to-head - - cat #for $q in $input1# $q #end for# > $out_file1 - + + + '$out_file1' + ]]> - + diff --git a/test/functional/tools/for_workflows/count_list.xml b/test/functional/tools/for_workflows/count_list.xml index abb56f955c37..f395d513f406 100644 --- a/test/functional/tools/for_workflows/count_list.xml +++ b/test/functional/tools/for_workflows/count_list.xml @@ -1,10 +1,10 @@ - + count the number of items in a list '$out_file1' +echo '${len($input1.keys())}' > '$out_file1' ]]> - + diff --git a/test/functional/tools/for_workflows/count_multi_file.xml b/test/functional/tools/for_workflows/count_multi_file.xml index c7a2c8ce1246..f998f52d2070 100644 --- a/test/functional/tools/for_workflows/count_multi_file.xml +++ b/test/functional/tools/for_workflows/count_multi_file.xml @@ -1,10 +1,10 @@ - + count the number of datasets in a multiple file input '$out_file1' +echo '${len($input1)}' > '$out_file1' ]]> - + diff --git a/test/functional/tools/for_workflows/head.xml b/test/functional/tools/for_workflows/head.xml index 2b2a550885e8..97183f3acc56 100644 --- a/test/functional/tools/for_workflows/head.xml +++ b/test/functional/tools/for_workflows/head.xml @@ -1,13 +1,17 @@ - - lines from a dataset - head -n $lineNum '$input' > '$out_file1' - - - - - - - - - + + lines from a dataset + '$out_file1' + ]]> + + + + + + + + + + + diff --git a/test/functional/tools/for_workflows/split.xml b/test/functional/tools/for_workflows/split.xml index def9c17a8d00..1420d6596895 100644 --- a/test/functional/tools/for_workflows/split.xml +++ b/test/functional/tools/for_workflows/split.xml @@ -1,33 +1,33 @@ - - bash $script - - - - mkdir outputs; - cd outputs; - i=1; - while read -r line || [[ -n "\$line" ]]; do - printf "\$line\n" > \$i ; - i=\$[\$i +1]; - done < "$input1"; - - - - - - - - - - - - - - - - - - - + + + \$i ; + i=\$[\$i +1]; +done < '$input1' + ]]> + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/gzipped_inputs.xml b/test/functional/tools/gzipped_inputs.xml index 5b73d34005bb..3e5bf113b80a 100644 --- a/test/functional/tools/gzipped_inputs.xml +++ b/test/functional/tools/gzipped_inputs.xml @@ -1,7 +1,7 @@ - - - cat $input1 > $out_file1 - + + '$out_file1' + ]]> diff --git a/test/functional/tools/identifier_in_conditional.xml b/test/functional/tools/identifier_in_conditional.xml index fd3c2372c8fa..6b912440c606 100644 --- a/test/functional/tools/identifier_in_conditional.xml +++ b/test/functional/tools/identifier_in_conditional.xml @@ -1,4 +1,4 @@ - + - + - + diff --git a/test/functional/tools/identifier_multiple.xml b/test/functional/tools/identifier_multiple.xml index 4fdac7468962..2b4446560a0e 100644 --- a/test/functional/tools/identifier_multiple.xml +++ b/test/functional/tools/identifier_multiple.xml @@ -1,15 +1,15 @@ - - - #for $input in $input1# + + > 'output1'; - #end for# - - - - - - - - - +#end for# + ]]> + + + + + + + + diff --git a/test/functional/tools/identifier_multiple_in_conditional.xml b/test/functional/tools/identifier_multiple_in_conditional.xml index f6f397ae51ab..81d12fd99fa4 100644 --- a/test/functional/tools/identifier_multiple_in_conditional.xml +++ b/test/functional/tools/identifier_multiple_in_conditional.xml @@ -1,25 +1,25 @@ - - + > 'output1'; - #end for# - ]]> - - - - - - - - - +#end for# + ]]> + + + + + + + + + + + - - - - - - - - + + + + + + diff --git a/test/functional/tools/identifier_multiple_in_repeat.xml b/test/functional/tools/identifier_multiple_in_repeat.xml index 90db71b9b53e..7b124b962dbc 100644 --- a/test/functional/tools/identifier_multiple_in_repeat.xml +++ b/test/functional/tools/identifier_multiple_in_repeat.xml @@ -1,27 +1,27 @@ - - + > 'output1'; - #end for# #end for# - ]]> - - - - - - - - - - - - - - - - - - +#end for# + ]]> + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/identifier_single.xml b/test/functional/tools/identifier_single.xml index 992873bed7cb..874c1fa71b6b 100644 --- a/test/functional/tools/identifier_single.xml +++ b/test/functional/tools/identifier_single.xml @@ -1,13 +1,13 @@ - - - echo '$input1.element_identifier' > 'output1' - - - - - - - - - + + 'output1' + ]]> + + + + + + + + diff --git a/test/functional/tools/identifier_single_in_repeat.xml b/test/functional/tools/identifier_single_in_repeat.xml index e973764a56fc..d82613b00e05 100644 --- a/test/functional/tools/identifier_single_in_repeat.xml +++ b/test/functional/tools/identifier_single_in_repeat.xml @@ -1,4 +1,4 @@ - + > 'output1'; @@ -9,10 +9,10 @@ - + - + diff --git a/test/functional/tools/identifier_source.xml b/test/functional/tools/identifier_source.xml index 871b0e025271..808aa39d8679 100644 --- a/test/functional/tools/identifier_source.xml +++ b/test/functional/tools/identifier_source.xml @@ -1,11 +1,9 @@ verifies identifier source can be specified from input - -'$outputA' && - cat '$inputA' '$inputB' > '$outputB' -]]> - + '$outputA' && +cat '$inputA' '$inputB' > '$outputB' + ]]> @@ -14,6 +12,8 @@ + + diff --git a/test/functional/tools/implicit_default_conds.xml b/test/functional/tools/implicit_default_conds.xml index 0a5fe3b7d77c..0040d73fbf2b 100644 --- a/test/functional/tools/implicit_default_conds.xml +++ b/test/functional/tools/implicit_default_conds.xml @@ -1,8 +1,8 @@ - - - echo "$param_group[0].p1.val" >> $out_file1; - echo "$param_group[0].p2.val" >> $out_file1; - + + '$out_file1' && +echo '$param_group[0].p2.val' >> '$out_file1' + ]]> @@ -11,10 +11,10 @@ - + - + @@ -23,10 +23,10 @@ - + - + diff --git a/test/functional/tools/job_environment_default.xml b/test/functional/tools/job_environment_default.xml index 61604b73e03c..46d87b26b577 100644 --- a/test/functional/tools/job_environment_default.xml +++ b/test/functional/tools/job_environment_default.xml @@ -1,16 +1,16 @@ - busybox:ubuntu-14.04 + busybox:ubuntu-14.04 &2 echo 'Example tool stderr output.'); - echo `id -u` > '$user_id'; - echo `id -g` > '$group_id'; - echo `pwd` > '$pwd'; - echo "\$HOME" > '$home'; - echo "\$TMP" > '$tmp'; - echo "\$SOME_ENV_VAR" > '$some_env_var'; +echo 'Writing environment properties to output files.' && +(>&2 echo 'Example tool stderr output.') && +echo \$(id -u) > '$user_id' && +echo \$(id -g) > '$group_id' && +echo \$(pwd) > '$pwd' && +echo "\$HOME" > '$home' && +echo "\$TMP" > '$tmp' && +echo "\$SOME_ENV_VAR" > '$some_env_var' ]]> @@ -22,6 +22,8 @@ + + diff --git a/test/functional/tools/job_environment_default_legacy.xml b/test/functional/tools/job_environment_default_legacy.xml index a00a661ebcac..8b5dc1f220ca 100644 --- a/test/functional/tools/job_environment_default_legacy.xml +++ b/test/functional/tools/job_environment_default_legacy.xml @@ -1,14 +1,14 @@ - busybox:ubuntu-14.04 + busybox:ubuntu-14.04 '$user_id'; - echo `id -g` > '$group_id'; - echo `pwd` > '$pwd'; - echo "\$HOME" > '$home'; - echo "\$TMP" > '$tmp'; - echo "\$SOME_ENV_VAR" > '$some_env_var'; +echo \$(id -u) > '$user_id' && +echo \$(id -g) > '$group_id' && +echo \$(pwd) > '$pwd' && +echo "\$HOME" > '$home' && +echo "\$TMP" > '$tmp' && +echo "\$SOME_ENV_VAR" > '$some_env_var' ]]> @@ -20,6 +20,8 @@ + + diff --git a/test/functional/tools/job_environment_explicit_isolated_home.xml b/test/functional/tools/job_environment_explicit_isolated_home.xml index ddcbc2e529c0..b00152aa361f 100644 --- a/test/functional/tools/job_environment_explicit_isolated_home.xml +++ b/test/functional/tools/job_environment_explicit_isolated_home.xml @@ -3,12 +3,12 @@ busybox:ubuntu-14.04 '$user_id'; -echo `id -g` > '$group_id'; -echo `pwd` > '$pwd'; -echo "\$HOME" > '$home'; -echo "\$TMP" > '$tmp'; -echo "\$SOME_ENV_VAR" > '$some_env_var'; +echo \$(id -u) > '$user_id' && +echo \$(id -g) > '$group_id' && +echo \$(pwd) > '$pwd' && +echo "\$HOME" > '$home' && +echo "\$TMP" > '$tmp' && +echo "\$SOME_ENV_VAR" > '$some_env_var' ]]> @@ -20,6 +20,8 @@ echo "\$SOME_ENV_VAR" > '$some_env_var'; + + diff --git a/test/functional/tools/job_environment_explicit_shared_home.xml b/test/functional/tools/job_environment_explicit_shared_home.xml index 65b40ad07745..d1ae5ab788c9 100644 --- a/test/functional/tools/job_environment_explicit_shared_home.xml +++ b/test/functional/tools/job_environment_explicit_shared_home.xml @@ -1,14 +1,14 @@ - busybox:ubuntu-14.04 + busybox:ubuntu-14.04 '$user_id'; - echo `id -g` > '$group_id'; - echo `pwd` > '$pwd'; - echo "\$HOME" > '$home'; - echo "\$TMP" > '$tmp'; - echo "\$SOME_ENV_VAR" > '$some_env_var'; +echo \$(id -u) > '$user_id' && +echo \$(id -g) > '$group_id' && +echo \$(pwd) > '$pwd' && +echo "\$HOME" > '$home' && +echo "\$TMP" > '$tmp' && +echo "\$SOME_ENV_VAR" > '$some_env_var' ]]> @@ -20,6 +20,8 @@ + + diff --git a/test/functional/tools/job_properties.xml b/test/functional/tools/job_properties.xml index 753aa026a255..12f0ca010496 100644 --- a/test/functional/tools/job_properties.xml +++ b/test/functional/tools/job_properties.xml @@ -1,25 +1,26 @@ - + echo 'v1.1' &2 && - echo "This is a line of text." > '$out_file1' && - cp '$out_file1' '$one' && - cp '$out_file1' '$two' - #else - echo "The bool is not true" && - echo "The bool is very not true" 1>&2 && - echo "This is a different line of text." > '$out_file1' && - sh -c "exit 2" - #end if - #if $failbool - ; sh -c "exit 127" - #end if - +#if $thebool + echo 'The bool is true' && + echo 'The bool is really true' 1>&2 && + echo 'This is a line of text.' > '$out_file1' && + cp '$out_file1' '$one' && + cp '$out_file1' '$two' +#else + echo 'The bool is not true' && + echo 'The bool is very not true' 1>&2 && + echo 'This is a different line of text.' > '$out_file1' && + sh -c 'exit 2' +#end if +#if $failbool + ## use ';' to concatenate commands so that the next one is run independently + ## of the exit code of the previous one + ; exit 127 +#end if ]]> diff --git a/test/functional/tools/metadata.xml b/test/functional/tools/metadata.xml index e9268b9f01c0..1b8e92647b5f 100644 --- a/test/functional/tools/metadata.xml +++ b/test/functional/tools/metadata.xml @@ -1,29 +1,34 @@ - mkdir $output_copy_of_input.extra_files_path; cp $input.extra_files_path/* $output_copy_of_input.extra_files_path; echo "$input.metadata.base_name" > $output_of_input_metadata - - - - - - - - - - - - - - - - - - - - - - - - - - - + '$output_of_input_metadata' + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/metadata_bcf.xml b/test/functional/tools/metadata_bcf.xml index 396a8bd7abda..0d643931d3d0 100644 --- a/test/functional/tools/metadata_bcf.xml +++ b/test/functional/tools/metadata_bcf.xml @@ -1,16 +1,18 @@ - file "${input_bcf.metadata.bcf_index}" > "${output_of_input_metadata}" + '${output_of_input_metadata}' + ]]> - + - + - - - - - + + + + + diff --git a/test/functional/tools/metadata_biom1.xml b/test/functional/tools/metadata_biom1.xml index 6777324c0865..3da80587a2f3 100644 --- a/test/functional/tools/metadata_biom1.xml +++ b/test/functional/tools/metadata_biom1.xml @@ -1,5 +1,7 @@ - cp "${input_metadata_values}" "${output_of_input_metadata}" + table_rows: ${input_biom1.metadata.table_rows} table_matrix_element_type: ${input_biom1.metadata.table_matrix_element_type} @@ -14,15 +16,15 @@ table_id: ${input_biom1.metadata.table_id} table_columns: ${input_biom1.metadata.table_columns} - + - + - - - - + + + + diff --git a/test/functional/tools/mulled_example_broken_no_requirements.xml b/test/functional/tools/mulled_example_broken_no_requirements.xml index bbe58578aa99..d6bbd0e8e6fa 100644 --- a/test/functional/tools/mulled_example_broken_no_requirements.xml +++ b/test/functional/tools/mulled_example_broken_no_requirements.xml @@ -10,16 +10,16 @@ $output_1 2>&1 +bwa > $output_1 2>&1 ]]> - + - - \ No newline at end of file + + diff --git a/test/functional/tools/mulled_example_explicit.xml b/test/functional/tools/mulled_example_explicit.xml index f341dae5bdae..03db8e436e5a 100644 --- a/test/functional/tools/mulled_example_explicit.xml +++ b/test/functional/tools/mulled_example_explicit.xml @@ -7,16 +7,16 @@ $output_1 2>&1 +bwa > $output_1 2>&1 ]]> - + - - \ No newline at end of file + + diff --git a/test/functional/tools/mulled_example_invalid_case.xml b/test/functional/tools/mulled_example_invalid_case.xml index f3d912bd53b3..ef9e6b896f35 100644 --- a/test/functional/tools/mulled_example_invalid_case.xml +++ b/test/functional/tools/mulled_example_invalid_case.xml @@ -9,16 +9,16 @@ $output_1 2>&1 +bwa > '$output_1' 2>&1 ]]> - + - - \ No newline at end of file + + diff --git a/test/functional/tools/mulled_example_multi_1.xml b/test/functional/tools/mulled_example_multi_1.xml index b5c2dae56feb..fe461d1a955e 100644 --- a/test/functional/tools/mulled_example_multi_1.xml +++ b/test/functional/tools/mulled_example_multi_1.xml @@ -18,10 +18,10 @@ bedtools '$out_file1' && - echo "Moo" >> '$out_file1' && - samtools >> '$out_file1' 2>&1 && - echo "Cow" >> '$out_file1' +bedtools --version > '$out_file1' && +echo "Moo" >> '$out_file1' && +samtools >> '$out_file1' 2>&1 && +echo "Cow" >> '$out_file1' ]]> @@ -29,10 +29,12 @@ - - This is an example mulled tool that combines bedtools and samtools in one - command-line invocation. - + + + 10.1093/bioinformatics/btq033 diff --git a/test/functional/tools/mulled_example_multi_incomplete.xml b/test/functional/tools/mulled_example_multi_incomplete.xml index be961895d70d..e0df3920357e 100644 --- a/test/functional/tools/mulled_example_multi_incomplete.xml +++ b/test/functional/tools/mulled_example_multi_incomplete.xml @@ -1,9 +1,9 @@ $out_file1 ; - echo "Moo" >> $out_file1 ; - samtools >> $out_file1 2>&1 ; - echo "Cow" >> $out_file1 ; +bedtools --version > '$out_file1' && +echo 'Moo' >> '$out_file1' && +samtools >> '$out_file1' 2>&1 && +echo 'Cow' >> '$out_file1' ]]> samtools diff --git a/test/functional/tools/mulled_example_multi_versionless.xml b/test/functional/tools/mulled_example_multi_versionless.xml index 396526ef39ba..2c9e45793dde 100644 --- a/test/functional/tools/mulled_example_multi_versionless.xml +++ b/test/functional/tools/mulled_example_multi_versionless.xml @@ -1,9 +1,9 @@ $out_file1 ; - echo "Moo" >> $out_file1 ; - samtools >> $out_file1 2>&1 ; - echo "Cow" >> $out_file1 ; +bedtools --version > '$out_file1' && +echo 'Moo' >> '$out_file1' && +samtools >> '$out_file1' 2>&1 && +echo 'Cow' >> '$out_file1' ]]> samtools diff --git a/test/functional/tools/mulled_example_simple.xml b/test/functional/tools/mulled_example_simple.xml index d061297a93fa..d92c2d2c5564 100644 --- a/test/functional/tools/mulled_example_simple.xml +++ b/test/functional/tools/mulled_example_simple.xml @@ -6,16 +6,16 @@ $output_1 2>&1 +bwa > '$output_1' 2>&1 ]]> - + + + - - - \ No newline at end of file + diff --git a/test/functional/tools/multi_repeats.xml b/test/functional/tools/multi_repeats.xml index 745cb8631156..1e0251276888 100644 --- a/test/functional/tools/multi_repeats.xml +++ b/test/functional/tools/multi_repeats.xml @@ -1,7 +1,7 @@ - - - cat $input1 #for $q in $queries# ${q.input2} #end for# #for $q in $more_queries# ${q.more_queries_input} #end for# > $out_file1 - + + '$out_file1' + ]]> diff --git a/test/functional/tools/multi_select.xml b/test/functional/tools/multi_select.xml index 0c5fd5635aac..9464430491cd 100644 --- a/test/functional/tools/multi_select.xml +++ b/test/functional/tools/multi_select.xml @@ -1,45 +1,50 @@ - multi_select - - ${select_ex} - - cat $config > $output; echo '$select_optional' > $output2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + multi_select + '$output' && +echo '$select_optional' > '$output2' + ]]> + + ${select_ex} + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/output_auto_format.xml b/test/functional/tools/output_auto_format.xml index 6a2c8f05123c..8dbcef7d380b 100644 --- a/test/functional/tools/output_auto_format.xml +++ b/test/functional/tools/output_auto_format.xml @@ -1,16 +1,17 @@ - cp $input 'out' - - - - - - - - - - - - - + + + + + + + + + + + + + diff --git a/test/functional/tools/output_filter.xml b/test/functional/tools/output_filter.xml index dfb179ef4ec7..2002fee03826 100644 --- a/test/functional/tools/output_filter.xml +++ b/test/functional/tools/output_filter.xml @@ -1,95 +1,174 @@ - test for output filtering and expect_num_outputs - - echo "test" > 1; - echo "test" > 2; - echo "test" > 3; - echo "test" > 4; - echo "test" > 5; - echo "test" > p1.forward; - echo "test" > p1.reverse; - echo "test" > p2.forward; - echo "test" > p2.reverse; - - - - - - - - - - produce_out_1 is True - - - filter_text_1 in ["foo", "bar"] - - filter_text_1 == "foo" - - - - - produce_collection is True - - - - produce_paired_collection is True - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + test for output filtering and expect_num_outputs + 1 && +echo 'test' > 2 && +echo 'test' > 3 && +echo 'test' > 4 && +echo 'test' > 5 && +echo 'test' > p1.forward && +echo 'test' > p1.reverse && +echo 'test' > p2.forward && +echo 'test' > p2.reverse + ]]> + + + + + + + + + produce_out_1 is True + + + filter_text_1 in ["foo", "bar"] + + filter_text_1 == "foo" + + + + + produce_collection is True + + + + produce_paired_collection is True + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - diff --git a/test/functional/tools/output_filter_exception_1.xml b/test/functional/tools/output_filter_exception_1.xml index 2bbef5d47f20..a6631c7190d6 100644 --- a/test/functional/tools/output_filter_exception_1.xml +++ b/test/functional/tools/output_filter_exception_1.xml @@ -1,35 +1,39 @@ - - echo "test" > 1; - echo "test" > 2; - echo "test" > 3; - echo "test" > 4; - echo "test" > 5; - - - - - - - - - - - - - - - - - - options['adv_opt1'] is True - - - - - - - - - - \ No newline at end of file + 1 && +echo 'test' > 2 + ]]> + + + + + + + + + + + + + + + + options['adv_opt1'] is True + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/output_filter_with_input.xml b/test/functional/tools/output_filter_with_input.xml index c8b115d05e44..b878555c8218 100644 --- a/test/functional/tools/output_filter_with_input.xml +++ b/test/functional/tools/output_filter_with_input.xml @@ -1,31 +1,29 @@ - - - echo "test" > 1; - echo "test" > 2; - echo "test" > 3; - echo "test" > 4; - echo "test" > 5; - - - - - - - - - produce_out_1 is True - - - filter_text_1 in ["foo", "bar"] - - filter_text_1 == "foo" - - - - input_1.ext != 'xyz' - - - - + + 1 && +echo 'test' > 2 && +echo 'test' > 3 + ]]> + + + + + + + + produce_out_1 is True + + + filter_text_1 in ["foo", "bar"] + + filter_text_1 == "foo" + + + + input_1.ext != 'xyz' + + + + diff --git a/test/functional/tools/output_format.xml b/test/functional/tools/output_format.xml index 8c5005879ef5..0a584c8cb061 100644 --- a/test/functional/tools/output_format.xml +++ b/test/functional/tools/output_format.xml @@ -1,74 +1,88 @@ - - echo "test" > 1; - echo "test" > 2; - echo "test" > 3; - echo "test" > 4; - echo "test" > 5; - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + 1 && +echo 'test' > 2 && +echo 'test' > 3 && +echo 'test' > 4 && +echo 'test' > 5 + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/output_format_collection.xml b/test/functional/tools/output_format_collection.xml index 179517983446..ea7a8114bf1f 100644 --- a/test/functional/tools/output_format_collection.xml +++ b/test/functional/tools/output_format_collection.xml @@ -1,35 +1,35 @@ - - echo "test" > 1; - echo "test" > 2; - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + 1 && +echo "test" > 2 + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/output_format_deprecated_when.xml b/test/functional/tools/output_format_deprecated_when.xml index 63cf1b406e10..bd439de7d5bd 100644 --- a/test/functional/tools/output_format_deprecated_when.xml +++ b/test/functional/tools/output_format_deprecated_when.xml @@ -1,30 +1,34 @@ - - echo "test" > 5; - - - - - - - - - - - - - - - - - - - - - - - - - - + 5 + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/output_order.xml b/test/functional/tools/output_order.xml index 0658735d6dd1..88f631aa6b9e 100644 --- a/test/functional/tools/output_order.xml +++ b/test/functional/tools/output_order.xml @@ -1,25 +1,28 @@ - echo $pa > $output_a; echo $pb > $output_b - - - - - - - - - - - - - - - - - - - - - - + '$output_a' && +echo $pb > '$output_b' + ]]> + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/parallelism.xml b/test/functional/tools/parallelism.xml index be0ec1dbde76..feafa0351cba 100644 --- a/test/functional/tools/parallelism.xml +++ b/test/functional/tools/parallelism.xml @@ -1,8 +1,8 @@ - + - - cat '$input1' > '$out_file1' - + '$out_file1' + ]]> diff --git a/test/functional/tools/parallelism_optional.xml b/test/functional/tools/parallelism_optional.xml index 4013b2735553..78e8bca47493 100644 --- a/test/functional/tools/parallelism_optional.xml +++ b/test/functional/tools/parallelism_optional.xml @@ -1,11 +1,11 @@ - + - - cat '$input1' > '$out_file1' - + '$out_file1' + ]]> - + diff --git a/test/functional/tools/param_text_option.xml b/test/functional/tools/param_text_option.xml index 21426556a14f..5fa52e0c216c 100644 --- a/test/functional/tools/param_text_option.xml +++ b/test/functional/tools/param_text_option.xml @@ -1,7 +1,7 @@ - - echo "$text_param" > $out_file1; - + $out_file1; + ]]> diff --git a/test/functional/tools/python_environment_problem.xml b/test/functional/tools/python_environment_problem.xml index dcc2961e1bc1..9eea39aa29fa 100644 --- a/test/functional/tools/python_environment_problem.xml +++ b/test/functional/tools/python_environment_problem.xml @@ -3,9 +3,9 @@ This script imports galaxy.eggs which is no longer available to tools by default. Only declared legacy tools have this available. --> - - python $__tool_directory__/python_environment_problem.py '$out_file1' - + diff --git a/test/functional/tools/qc_stdout.xml b/test/functional/tools/qc_stdout.xml index c02dc2c94509..634f48a6396b 100644 --- a/test/functional/tools/qc_stdout.xml +++ b/test/functional/tools/qc_stdout.xml @@ -3,11 +3,11 @@ &2 echo "my standard error" +cp '$input' '$output' && +echo "Some example stdout........" && +echo "Quality of sample is ${int($quality) * 10}%." && +echo "Some more example stdout........" && +>&2 echo "my standard error" ]]> diff --git a/test/functional/tools/sam_to_bam.xml b/test/functional/tools/sam_to_bam.xml index 46b92f2a208a..b01152a76707 100644 --- a/test/functional/tools/sam_to_bam.xml +++ b/test/functional/tools/sam_to_bam.xml @@ -1,7 +1,7 @@ - - cat '$input1' > '$out_file1' - + '$out_file1' + ]]> diff --git a/test/functional/tools/section.xml b/test/functional/tools/section.xml index 29bb7fe10e3d..874f2c09be69 100644 --- a/test/functional/tools/section.xml +++ b/test/functional/tools/section.xml @@ -1,8 +1,8 @@ - - - echo "$int.inttest" >> $out_file1; - echo "$float.floattest" >> $out_file1; - + + '$out_file1' && +echo $float.floattest >> '$out_file1' + ]]>
diff --git a/test/functional/tools/select_from_dataset.xml b/test/functional/tools/select_from_dataset.xml index 3e1c6382529a..3a67ac01db8a 100644 --- a/test/functional/tools/select_from_dataset.xml +++ b/test/functional/tools/select_from_dataset.xml @@ -1,39 +1,39 @@ Create dynamic options from data sets '$output' && - echo select_multiple $select_multiple >> '$output' && - echo select_collection $select_collection >> '$output' +echo select_single '$select_single' > '$output' && +echo select_multiple '$select_multiple' >> '$output' && +echo select_collection '$select_collection' >> '$output' ]]> - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - + @@ -58,7 +58,6 @@ - diff --git a/test/functional/tools/simple_constructs.xml b/test/functional/tools/simple_constructs.xml index eabf6e949cdd..f72036d7500d 100644 --- a/test/functional/tools/simple_constructs.xml +++ b/test/functional/tools/simple_constructs.xml @@ -1,16 +1,16 @@ - - echo "$p1.p1val" >> $out_file1; - echo "$booltest" >> $out_file1; - echo "$inttest" >> $out_file1; - echo "$floattest" >> $out_file1; - echo "$radio_select" >> $out_file1; - echo "$check_select" >> $out_file1; - echo "$drop_select" >> $out_file1; - #if len($files) > 0 - cat "$files[0].file" >> $out_file1; - #end if - + '$out_file1' && +echo $booltest >> '$out_file1' && +echo $inttest >> '$out_file1' && +echo $floattest >> '$out_file1' && +echo $radio_select >> '$out_file1' && +echo $check_select >> '$out_file1' && +echo $drop_select >> '$out_file1' && +#if len($files) > 0 + cat '$files[0].file' >> '$out_file1' +#end if + ]]> diff --git a/test/functional/tools/special_params.xml b/test/functional/tools/special_params.xml index 464b21817af4..83cbb21d5ec6 100644 --- a/test/functional/tools/special_params.xml +++ b/test/functional/tools/special_params.xml @@ -1,36 +1,44 @@ - echo $__root_dir__ > out_root_dir; - echo $__datatypes_config__ > out_datatypes_config; - echo $__admin_users__ > out_admin_users; - echo $__user_email__ > out_user_email - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + out_root_dir && +echo '$__datatypes_config__' > out_datatypes_config && +echo '$__admin_users__' > out_admin_users && +echo '$__user_email__' > out_user_email + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/strict_shell.xml b/test/functional/tools/strict_shell.xml index 58626c972515..0a6adab9ae29 100644 --- a/test/functional/tools/strict_shell.xml +++ b/test/functional/tools/strict_shell.xml @@ -1,9 +1,9 @@ - - echo "Hello" > $out_file1 - ; sh -c "exit $exit_code" - ; sh -c "exit 0" - + '$out_file1'; +sh -c 'exit $exit_code'; +sh -c 'exit 0' + ]]> diff --git a/test/functional/tools/strict_shell_default_off.xml b/test/functional/tools/strict_shell_default_off.xml index 50d1751b9244..aca66494dc7c 100644 --- a/test/functional/tools/strict_shell_default_off.xml +++ b/test/functional/tools/strict_shell_default_off.xml @@ -1,9 +1,9 @@ - - echo "Hello" > $out_file1 - ; sh -c "exit $exit_code" - ; sh -c "exit 0" - + '$out_file1' +; sh -c 'exit $exit_code' +; sh -c 'exit 0' + ]]> diff --git a/test/functional/tools/strict_shell_profile.xml b/test/functional/tools/strict_shell_profile.xml index eb03d4517ca4..726e9d5a9fe0 100644 --- a/test/functional/tools/strict_shell_profile.xml +++ b/test/functional/tools/strict_shell_profile.xml @@ -1,9 +1,9 @@ - - echo "Hello" > $out_file1 - ; sh -c "exit $exit_code" - ; sh -c "exit 0" - + '$out_file1' +; sh -c 'exit $exit_code' +; sh -c 'exit 0' + ]]> diff --git a/test/functional/tools/tool_directory.xml b/test/functional/tools/tool_directory.xml index 53532f531bb0..49734273e8bf 100644 --- a/test/functional/tools/tool_directory.xml +++ b/test/functional/tools/tool_directory.xml @@ -1,20 +1,19 @@ - - - cp $__tool_directory__/tool_directory.xml output1 - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/tool_provided_metadata_1.xml b/test/functional/tools/tool_provided_metadata_1.xml index a573a7091a9f..1a503b18eb31 100644 --- a/test/functional/tools/tool_provided_metadata_1.xml +++ b/test/functional/tools/tool_provided_metadata_1.xml @@ -1,30 +1,28 @@ - + - - echo "This is a line of text." > $out1; - cp $c1 galaxy.json; - + '$out1' && +cp '$c1' galaxy.json + ]]> - {"type": "dataset", "dataset_id": $out1.dataset.dataset.id, "name": "my dynamic name", "ext": "txt", "info": "my dynamic info", "dbkey": "cust1"} + {"type": "dataset", "dataset_id": $out1.dataset.dataset.id, "name": "my dynamic name", "ext": "txt", "info": "my dynamic info", "dbkey": "cust1"} - - - - - - - - - - - + + + + + + + + + diff --git a/test/functional/tools/tool_provided_metadata_10.xml b/test/functional/tools/tool_provided_metadata_10.xml index fce8be2f042c..f943f98514da 100644 --- a/test/functional/tools/tool_provided_metadata_10.xml +++ b/test/functional/tools/tool_provided_metadata_10.xml @@ -1,38 +1,38 @@ - - - echo "1" > sample1.report.tsv; - cp $c1 galaxy.json; - - - {"sample": { + + sample1.report.tsv && +cp '$c1' galaxy.json + ]]> + + {"sample": { "datasets": [ {"filename": "sample1.report.tsv", "name": "cool name 1", "ext": "txt", "info": "cool 1 info", "dbkey": "hg19", "metadata": {"data_lines": 10}} ] }} - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/tool_provided_metadata_11.xml b/test/functional/tools/tool_provided_metadata_11.xml index 415816ac9c4a..674b9724a380 100644 --- a/test/functional/tools/tool_provided_metadata_11.xml +++ b/test/functional/tools/tool_provided_metadata_11.xml @@ -1,41 +1,45 @@ - - - - mkdir sample1data; - echo "1" > sample1.report.tsv; - echo "foo line" > sample1data/foo; - echo "moo cow bar" > sample1data/bar; - cp $c1 galaxy.json; - - - {"type": "new_primary_dataset", "filename": "sample1.report.tsv", "name": "cool name 1", "ext": "txt", "info": "cool 1 info", "dbkey": "hg19", "extra_files": "sample1data"} + + + sample1.report.tsv && +echo 'foo line' > sample1data/foo && +echo 'moo cow bar' > sample1data/bar && +cp '$c1' galaxy.json + ]]> + + {"type": "new_primary_dataset", "filename": "sample1.report.tsv", "name": "cool name 1", "ext": "txt", "info": "cool 1 info", "dbkey": "hg19", "extra_files": "sample1data"} - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/tool_provided_metadata_12.xml b/test/functional/tools/tool_provided_metadata_12.xml index c38877850757..70a24f6715d6 100644 --- a/test/functional/tools/tool_provided_metadata_12.xml +++ b/test/functional/tools/tool_provided_metadata_12.xml @@ -1,45 +1,51 @@ - - - mkdir sample1data; - echo "1" > sample1.report.tsv; - echo "foo line" > sample1data/foo; - echo "moo cow bar" > sample1data/bar; - cp $c1 galaxy.json; - - - {"sample": { + + sample1.report.tsv && +echo 'foo line' > sample1data/foo && +echo 'moo cow bar' > sample1data/bar && +cp '$c1' galaxy.json + ]]> + + {"sample": { "datasets": [ {"filename": "sample1.report.tsv", "name": "cool name 1", "ext": "txt", "info": "cool 1 info", "dbkey": "hg19", "extra_files": "sample1data"} ] }} - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/tool_provided_metadata_2.xml b/test/functional/tools/tool_provided_metadata_2.xml index 9eca149cb81f..dce7a2144bc3 100644 --- a/test/functional/tools/tool_provided_metadata_2.xml +++ b/test/functional/tools/tool_provided_metadata_2.xml @@ -1,39 +1,41 @@ - - - - echo "1" > sample1.report.tsv; - echo "2" > sample2.report.tsv; - cp $c1 galaxy.json; - - - {"type": "new_primary_dataset", "filename": "sample1.report.tsv", "name": "cool name 1", "ext": "txt", "info": "cool 1 info", "dbkey": "hg19"} + + + sample1.report.tsv && +echo '2' > sample2.report.tsv && +cp '$c1' galaxy.json + ]]> + + {"type": "new_primary_dataset", "filename": "sample1.report.tsv", "name": "cool name 1", "ext": "txt", "info": "cool 1 info", "dbkey": "hg19"} {"type": "new_primary_dataset", "filename": "sample2.report.tsv", "name": "cool name 2", "ext": "txt", "info": "cool 2 info", "dbkey": "hg19"} - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/tool_provided_metadata_3.xml b/test/functional/tools/tool_provided_metadata_3.xml index f3ec2ac29e4f..6a2502112409 100644 --- a/test/functional/tools/tool_provided_metadata_3.xml +++ b/test/functional/tools/tool_provided_metadata_3.xml @@ -1,44 +1,46 @@ - - - - echo "1" > sample1.report.tsv; - echo "2" > sample2.report.tsv; - cp $c1 galaxy.json; - - - {"type": "new_primary_dataset", "filename": "sample1.report.tsv", "name": "cool name 1", "ext": "txt", "info": "cool 1 info", "dbkey": "hg19", "metadata": {"data_lines": 10, "foo": "bar"}} + + + sample1.report.tsv && +echo '2' > sample2.report.tsv && +cp '$c1' galaxy.json + ]]> + + {"type": "new_primary_dataset", "filename": "sample1.report.tsv", "name": "cool name 1", "ext": "txt", "info": "cool 1 info", "dbkey": "hg19", "metadata": {"data_lines": 10, "foo": "bar"}} {"type": "new_primary_dataset", "filename": "sample2.report.tsv", "name": "cool name 2", "ext": "txt", "info": "cool 2 info", "dbkey": "hg19", "metadata": {"data_lines": 20, "foo": "bar"}} - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/tool_provided_metadata_4.xml b/test/functional/tools/tool_provided_metadata_4.xml index 15cafddcc6a9..7fa68670fa76 100644 --- a/test/functional/tools/tool_provided_metadata_4.xml +++ b/test/functional/tools/tool_provided_metadata_4.xml @@ -1,31 +1,29 @@ - - echo "This is a line of text." > '$out1'; - cp $c1 galaxy.json; - + '$out1' && +cp '$c1' galaxy.json + ]]> - #import os + #import os {"type": "dataset", "dataset": "${os.path.basename(str($out1))}", "name": "my dynamic name", "ext": "txt", "info": "my dynamic info", "dbkey": "cust1"} - - - - - - - - - - - + + + + + + + + + diff --git a/test/functional/tools/tool_provided_metadata_5.xml b/test/functional/tools/tool_provided_metadata_5.xml index 33b527c4f307..3a81d1ce4a33 100644 --- a/test/functional/tools/tool_provided_metadata_5.xml +++ b/test/functional/tools/tool_provided_metadata_5.xml @@ -1,9 +1,9 @@ - - echo "This is a line of text." > $out1; - cp $c1 galaxy.json; - + '$out1' && +cp '$c1' galaxy.json + ]]> {"out1": { "name": "my dynamic name", @@ -14,23 +14,21 @@ - - - - - - - - - - - + + + + + + + + + diff --git a/test/functional/tools/tool_provided_metadata_6.xml b/test/functional/tools/tool_provided_metadata_6.xml index 78e9f3c36ca5..9743be9a4c63 100644 --- a/test/functional/tools/tool_provided_metadata_6.xml +++ b/test/functional/tools/tool_provided_metadata_6.xml @@ -1,10 +1,10 @@ - - - echo "1" > sample1.report.tsv; - echo "2" > sample2.report.tsv; - cp $c1 galaxy.json; - + + sample1.report.tsv && +echo '2' > sample2.report.tsv && +cp '$c1' galaxy.json + ]]> {"sample": { "datasets": [ @@ -13,31 +13,33 @@ ] }} - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/tool_provided_metadata_7.xml b/test/functional/tools/tool_provided_metadata_7.xml index a50adbfe2c3e..f7faa251ed61 100644 --- a/test/functional/tools/tool_provided_metadata_7.xml +++ b/test/functional/tools/tool_provided_metadata_7.xml @@ -1,43 +1,45 @@ - - - echo "1" > sample1.report.tsv; - echo "2" > sample2.report.tsv; - cp $c1 galaxy.json; - - - {"sample": { + + sample1.report.tsv && +echo '2' > sample2.report.tsv && +cp '$c1' galaxy.json + ]]> + + {"sample": { "datasets": [ {"filename": "sample1.report.tsv", "designation": "sample1", "name": "cool name 1", "ext": "txt", "info": "cool 1 info", "dbkey": "hg19"}, {"filename": "sample2.report.tsv", "designation": "sample2", "name": "cool name 2", "ext": "txt", "info": "cool 2 info", "dbkey": "hg19"} ] }} - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/tool_provided_metadata_8.xml b/test/functional/tools/tool_provided_metadata_8.xml index 60199cf0c4b7..1465e2821791 100644 --- a/test/functional/tools/tool_provided_metadata_8.xml +++ b/test/functional/tools/tool_provided_metadata_8.xml @@ -1,31 +1,29 @@ - - echo "This is a line of text." > $out1; - cp $c1 galaxy.json; - + '$out1' && +cp '$c1' galaxy.json; + ]]> - {"type": "dataset", "dataset_id": $out1.dataset.dataset.id, "name": "my dynamic name", "ext": "txt", "info": "my dynamic info", "dbkey": "cust1"} + {"type": "dataset", "dataset_id": $out1.dataset.dataset.id, "name": "my dynamic name", "ext": "txt", "info": "my dynamic info", "dbkey": "cust1"} - - - - - - - - - - - + + + + + + + + + diff --git a/test/functional/tools/tool_provided_metadata_9.xml b/test/functional/tools/tool_provided_metadata_9.xml index 285d5c880894..0d1b629449a0 100644 --- a/test/functional/tools/tool_provided_metadata_9.xml +++ b/test/functional/tools/tool_provided_metadata_9.xml @@ -1,12 +1,12 @@ - - echo "This is a line of text." > $out1; - cp $c1 not_galaxy.json; - + '$out1' && +cp '$c1' not_galaxy.json + ]]> - {"out1": { + {"out1": { "name": "my dynamic name", "ext": "txt", "info": "my dynamic info", @@ -16,22 +16,20 @@ - - - - - - - - - - - - + + + + + + + + + + diff --git a/test/functional/tools/top_level_data.xml b/test/functional/tools/top_level_data.xml index 37d2ba7e00e3..853ffd0ec9e2 100644 --- a/test/functional/tools/top_level_data.xml +++ b/test/functional/tools/top_level_data.xml @@ -1,34 +1,34 @@ - - cat '${f1}' >> $out1; - echo '${library.f2}' >> $out2; - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + > '$out1' && +echo '${library.f2}' >> '$out2' ## cannot use just f2 here + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/unicode_stream.xml b/test/functional/tools/unicode_stream.xml index 623b83a61be9..45b14677ddde 100644 --- a/test/functional/tools/unicode_stream.xml +++ b/test/functional/tools/unicode_stream.xml @@ -1,23 +1,25 @@ - echo "\x00" + $out_file1; + echo "\x00" > '$out_file1' && #end if -echo '$input1' >> '$out_file1'; -cat '$cf'; -echo "\x00"; ->&2 cat '$cf'; -sh -c "exit $exit" +echo '$input1' >> '$out_file1' && +cat '$cf' && +echo "\x00" && +>&2 cat '$cf' && +sh -c 'exit $exit' ]]> ვეპხის ტყაოსანი შოთა რუსთაველი - + diff --git a/test/functional/tools/validation_default.xml b/test/functional/tools/validation_default.xml index e0b64b28369a..94cd5b8f0aa0 100644 --- a/test/functional/tools/validation_default.xml +++ b/test/functional/tools/validation_default.xml @@ -1,39 +1,39 @@ - - echo '$input1' > out1; - echo $float_param > out2; - echo $select_param > out3; - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + out1 && +echo $float_param > out2 && +echo $select_param > out3 + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/validation_empty_dataset.xml b/test/functional/tools/validation_empty_dataset.xml index 589121bb1dc4..010f2bdd32d5 100644 --- a/test/functional/tools/validation_empty_dataset.xml +++ b/test/functional/tools/validation_empty_dataset.xml @@ -1,17 +1,17 @@ - - - echo "Hello World" > out1; - - - - - - - - - - - - - + + out1 + ]]> + + + + + + + + + + + + diff --git a/test/functional/tools/validation_hdf5.xml b/test/functional/tools/validation_hdf5.xml index d3cd9f9175b6..92f0011e22d7 100644 --- a/test/functional/tools/validation_hdf5.xml +++ b/test/functional/tools/validation_hdf5.xml @@ -1,7 +1,7 @@ - - cp '$input' '$output' - + diff --git a/test/functional/tools/validation_metadata_in_range.xml b/test/functional/tools/validation_metadata_in_range.xml index 327333817b37..1595efd816aa 100644 --- a/test/functional/tools/validation_metadata_in_range.xml +++ b/test/functional/tools/validation_metadata_in_range.xml @@ -1,30 +1,30 @@ - - echo "Hello World" > out1; - - - - - - - - - - - - - - - - - - - - - - - - - - + out1 + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/validation_repeat.xml b/test/functional/tools/validation_repeat.xml index ad9ee1b59046..45cf39b16e3c 100644 --- a/test/functional/tools/validation_repeat.xml +++ b/test/functional/tools/validation_repeat.xml @@ -1,57 +1,57 @@ - - - #for $r in $r1 - echo "${r.text}" >> out1; - #end for - #for $r in $r2 - echo "${r.text}" >> out2; - #end for - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + > out1; +#end for +#for $r in $r2 + echo '${r.text}' >> out2; +#end for + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/validation_sanitizer.xml b/test/functional/tools/validation_sanitizer.xml index e8a47a82108e..85c529ecadeb 100644 --- a/test/functional/tools/validation_sanitizer.xml +++ b/test/functional/tools/validation_sanitizer.xml @@ -1,35 +1,35 @@ - - - echo "${text}" >> out1; - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + > out1 + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/validation_tar.xml b/test/functional/tools/validation_tar.xml index 58ebd6ac0d69..9c37de7b5775 100644 --- a/test/functional/tools/validation_tar.xml +++ b/test/functional/tools/validation_tar.xml @@ -1,7 +1,7 @@ - - cat '$input' > '$output' - + '$output' + ]]> diff --git a/test/functional/tools/validation_tar_gz.xml b/test/functional/tools/validation_tar_gz.xml index cd18f43d2479..e10a3e07c90e 100644 --- a/test/functional/tools/validation_tar_gz.xml +++ b/test/functional/tools/validation_tar_gz.xml @@ -1,7 +1,7 @@ - - cat '$input' > '$output' - + '$output' + ]]> diff --git a/test/functional/tools/validation_zip.xml b/test/functional/tools/validation_zip.xml index 6e5120745405..ad9d94fafc47 100644 --- a/test/functional/tools/validation_zip.xml +++ b/test/functional/tools/validation_zip.xml @@ -1,7 +1,7 @@ - - cat '$input' > '$output' - + '$output' + ]]> diff --git a/test/functional/tools/vcf_bgzip.xml b/test/functional/tools/vcf_bgzip.xml index 070be227ee00..f43429bc0c58 100644 --- a/test/functional/tools/vcf_bgzip.xml +++ b/test/functional/tools/vcf_bgzip.xml @@ -1,18 +1,18 @@ - + - + - - - - - - + + + + + + diff --git a/test/functional/tools/version_command_interpreter.xml b/test/functional/tools/version_command_interpreter.xml index 15b6ce8567db..9b4fd5fd00b8 100644 --- a/test/functional/tools/version_command_interpreter.xml +++ b/test/functional/tools/version_command_interpreter.xml @@ -1,10 +1,10 @@ - - version_command.py - - - cp $input $output - + + diff --git a/test/functional/tools/version_command_plain.xml b/test/functional/tools/version_command_plain.xml index 8211fde9b6b0..8eb4e6904db2 100644 --- a/test/functional/tools/version_command_plain.xml +++ b/test/functional/tools/version_command_plain.xml @@ -1,10 +1,10 @@ - - echo "4.0.0" - - - cp $input $output - + + diff --git a/test/functional/tools/version_command_tool_dir.xml b/test/functional/tools/version_command_tool_dir.xml index 87023ee1a634..dc4a40ca1694 100644 --- a/test/functional/tools/version_command_tool_dir.xml +++ b/test/functional/tools/version_command_tool_dir.xml @@ -1,10 +1,10 @@ - - python $__tool_directory__/version_command.py - - - cp $input $output - + +