Mercurial > repos > peterjc > effectivet3
changeset 29:35c358aa7801 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 37d5b47ec23e2cbaa453cc660bb1fcbb10dd34ee-dirty
| author | peterjc |
|---|---|
| date | Wed, 17 May 2017 11:16:58 -0400 |
| parents | d6976a4c055b |
| children | 007e86eff414 |
| files | tools/effectiveT3/README.rst tools/effectiveT3/effectiveT3.py tools/effectiveT3/effectiveT3.xml |
| diffstat | 3 files changed, 4 insertions(+), 3 deletions(-) [+] |
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--- a/tools/effectiveT3/README.rst Thu May 11 12:44:17 2017 -0400 +++ b/tools/effectiveT3/README.rst Wed May 17 11:16:58 2017 -0400 @@ -98,6 +98,7 @@ - Minor internal changes to Python script for error reporting & style. v0.0.18 - Use ``<command detect_errors="aggressive">`` (internal change only). - Single quote command line arguments (internal change only). +v0.0.19 - Python 3 compatible exception handling. ======= ======================================================================
--- a/tools/effectiveT3/effectiveT3.py Thu May 11 12:44:17 2017 -0400 +++ b/tools/effectiveT3/effectiveT3.py Wed May 17 11:16:58 2017 -0400 @@ -21,7 +21,7 @@ if "-v" in sys.argv or "--version" in sys.argv: # TODO - Get version of the JAR file dynamically? - print("Wrapper v0.0.17, TTSS_GUI-1.0.1.jar") + print("Wrapper v0.0.19, TTSS_GUI-1.0.1.jar") sys.exit(0) if len(sys.argv) != 5: @@ -74,7 +74,7 @@ # script is killed, so too is the child process. try: child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) - except Exception, err: + except Exception as err: sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) # Use .communicate as can get deadlocks with .wait(), stdout, stderr = child.communicate()
--- a/tools/effectiveT3/effectiveT3.xml Thu May 11 12:44:17 2017 -0400 +++ b/tools/effectiveT3/effectiveT3.xml Wed May 17 11:16:58 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="effectiveT3" name="Effective T3" version="0.0.18"> +<tool id="effectiveT3" name="Effective T3" version="0.0.19"> <description>Find bacterial effectors in protein sequences</description> <requirements> <requirement type="package" version="1.0.1">effectiveT3</requirement>