diff --git a/.gitignore b/.gitignore new file mode 100644 index 000000000..337b26b54 --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +tool_test_output.html +tool_test_output.json \ No newline at end of file diff --git a/.travis.yml b/.travis.yml index 91d923040..5945e61a9 100644 --- a/.travis.yml +++ b/.travis.yml @@ -5,19 +5,21 @@ # See http://travis-ci.org/ for details language: python -before_install: - - export WRAPPER_REPO="galaxy/metaMS" - - export GALAXY_RELEASE="release_17.01" - - export PLANEMO_RELEASE="0.37.0" +env: + - TESTFOLDER=tools/metaMS_runGC + - TESTFOLDER=tools/metaMS_plot -install: +before_install: - sudo apt-get install -y python-virtualenv - virtualenv planemo-venv - . planemo-venv/bin/activate - - pip install --upgrade pip setuptools - - pip install planemo==$PLANEMO_RELEASE + - pip install planemo==0.58.1 +# @TODO: remove ASAP +# The issue: https://github.com/galaxyproject/planemo/issues/865 +install: + - for LINK in $(find ${TRAVIS_BUILD_DIR}/${TESTFOLDER}/test-data/ -type l -exec ls {} \;); do REALPATH=$(readlink -f $LINK); rm -f $LINK; cp $REALPATH $LINK; done script: - - planemo lint "${TRAVIS_BUILD_DIR}/${WRAPPER_REPO}" - - planemo test --conda_auto_init --conda_auto_install --conda_dependency_resolution --galaxy_branch "$GALAXY_RELEASE" --no_cache_galaxy "${TRAVIS_BUILD_DIR}/${WRAPPER_REPO}" + - planemo lint "${TRAVIS_BUILD_DIR}/${TESTFOLDER}" + - planemo test --galaxy_branch release_18.05 --no_cache_galaxy "${TRAVIS_BUILD_DIR}/${TESTFOLDER}" diff --git a/tools/macro/macros.xml b/tools/macro/macros.xml new file mode 100644 index 000000000..c2140399f --- /dev/null +++ b/tools/macro/macros.xml @@ -0,0 +1,77 @@ + + + + + + + + + + + + + bioconductor-metams + r-batch + + + + +
+ + + + + + + + + + + +
+
+ + + + +
+ + + + +
+
+ + + LC_ALL=C Rscript $__tool_directory__/ + + + ; + return=\$?; + cat 'log.txt'; + sh -c "exit \$return" + + + + + + #if $file_load_section.file_load_conditional.file_load_select == "yes": + #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"): + #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] ) + #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] ) + + singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' + #else + zipfile '$file_load_section.file_load_conditional.input' + #end if + #end if + + +
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