Improved CTD to galaxy conversion

.travis.yml

@@ -0,0 +1,58 @@
+language: python
+python:
+  - "3.6"
+
+install:
+  - sudo apt-get update
+#   - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+#       wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
+#     else
+#       wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+#     fi
+#   - bash miniconda.sh -b -p $HOME/miniconda
+#   - export PATH="$HOME/miniconda/bin:$PATH"
+#   - hash -r
+#   - conda config --set always_yes yes --set changeps1 no --set auto_activate_base False
+#   - conda update -q conda
+#   - conda init
+#   - source activate 
+#   - conda info -a
+#   
+# #   - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION
+# #   - source activate test-environment
+#   - conda config --add channels conda-forge
+#   - conda config --add channels bioconda
+#   - conda config --add channels anaconda
+#   - conda config --add channels workflowconversion
+# 
+#   - conda install python=$TRAVIS_PYTHON_VERSION
+#   # TODO could be replaced by conda package once it is merged and released
+#   - git clone -b topic/no-1-2x https://github.com/bernt-matthias/CTDopts $HOME/CTDopts
+#   - cd $HOME/CTDopts
+#   - python setup.py install 
+#   - conda install -c conda-forge lxml
+#   - conda install -c conda-forge ruamel.yaml 
+#   - conda install libxml2
+#   - cd $TRAVIS_BUILD_DIR
+#   - python setup.py install
+#   - conda install coverage green codecov
+
+#   - virtualenv .venv
+#   - . .venv/bin/activate
+  - pip install git+https://github.com/bernt-matthias/CTDopts@topic/no-1-2x
+  - pip install lxml ruamel.yaml planemo 
+  - cd $TRAVIS_BUILD_DIR
+  - python setup.py install
+script:
+  - python setup.py test
+# TODO fail expected due to 
+# https://github.com/galaxyproject/galaxy/pull/9081 which will be in 20.01 and 
+# empty.xml (no inputs) could be removed and  
+# - planemo l tests/test-data/
+
+  # planemo test content of tests/test-data (this is OK, because the previous
+  # tests ensure equality of the xmls that are generated and those in the package)
+  - export PATH=$(pwd)/tests/test-data:$PATH && planemo t tests/test-data/
+
+# after_script:
+# - python -m codecov

README.md

@@ -178,7 +178,33 @@ CTDs can contain an `<executablePath>` element that will be used when executing
 The following invocation of the converter will use `/opt/suite/bin` as a prefix when providing the executable path in the output files for any input CTD that lacks the `<executablePath>` section:
 
     $ python convert.py [FORMAT] -x /opt/suite/bin ...
-
+
+### Bump wrapper versions
+
+There are two ways to bump tool versions.  
+
+- Definition of a `@GALAXY_VERSION@` token in the macros file. This can be used to bump all tools at once. Tool versions will be `@TOOL_VERSION@+galaxy@GALAXY_VERSION@`.
+- Use the `--bump-file` parameter to specify the wrapper version of a subset of the tools in a json file that maps tool names/ids to a wrapper version. Tool version will be set to `@TOOL_VERSION@+galaxyX`, where `X` is the version found in the json file or `0` if not found.
+
+In case of an update of the tool version, i.e. `@TOOL_VERSION@`, in the first case `@GALAXY_VERSION@` should be reset to 0 and the dictionary in the bump file should be emptied otherwise.
+
+Rationale: the auto-generation of the tool xml files would overwrite the
+wrapper version when regenerated. Hence it needs to be specified externally,
+e.g. in the macros.xml or in the bump file.
+
+### Tests
+
+Tests for Galaxy tools are generated with:
+
+```
+PATH=$(pwd)/tests/test-data/:$PATH
+for i in tests/test-data/*ctd
+do
+b=$(basename $i .ctd)
+python convert.py galaxy -i tests/test-data/$b.ctd -o tests/test-data/$b.xml -m tests/test-data/macros.xml -f tests/test-data/filetypes.txt --test-test -p tests/test-data/hardcoded_params.json  --tool-version 5.0.011
+done
+```
+
 
 [CTDopts]: https://github.com/genericworkflownodes/CTDopts
 [CTDSchema]: https://github.com/WorkflowConversion/CTDSchema

common/exceptions.py

@@ -42,4 +42,4 @@ def __str__(self):
         return self.msg
 
     def __unicode__(self):
-        return self.msg
+        return self.msg