On 28.07.2014 12:22, Peter Cock wrote:

This is standard behaviour to prevent special characters being used
to construct malicious command lines. It can be configured within
your tool definition using the <sanitizer> tag set:

https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_set

Peter


Thanks a lot, Peter, that solved my problem !

Unfortunately, with this one fixed I now run into an additional one:

There is one free-text text field defined in my tool, which should accept characters outside the standard ascii code range (i.e. > 127), in particular, German Umlaute äöüÄÖÜ.
They are now no longer translated to Xs, but instead I get:

an 'ascii' codec can't decode byte 0xc3 in position 22: ordinal not in range(128) error, while parsing the content of the field inside the <command> tag. Is there any way to make Galaxy work with things outside the ascii range (like by using a different codec)?

Just in case, here is the complete traceback I'm seeing:

Traceback (most recent call last):
File "/home/galaxy/WMGalaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 152, in prepare_job
    job_wrapper.prepare()
File "/home/galaxy/WMGalaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 679, in prepare
    self.command_line, self.extra_filenames = tool_evaluator.build()
File "/home/galaxy/WMGalaxy/galaxy-dist/lib/galaxy/tools/evaluation.py", line 323, in build
    self.__build_command_line( )
File "/home/galaxy/WMGalaxy/galaxy-dist/lib/galaxy/tools/evaluation.py", line 339, in __build_command_line
    command_line = fill_template( command, context=param_dict )
File "/home/galaxy/WMGalaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template
    return str( Template( source=template_text, searchList=[context] ) )
File "/home/galaxy/WMGalaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__
    return getattr(self, mainMethName)()
File "cheetah_DynamicallyCompiledCheetahTemplate_1406545596_05_93125.py", line 163, in respond File "/home/galaxy/WMGalaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/DummyTransaction.py", line 47, in getvalue
    (%s)''' % (nonunicode, ex))
DummyResponseFailure: Looks like you're trying to mix encoded strings with Unicode strings
            (most likely utf-8 encoded ones)

This can happen if you're using the `EncodeUnicode` filter, or if you're manually encoding strings as utf-8 before passing them in on the searchList (possible offenders: ['ascii', 'ascii', ' ', 'non-ASCII characters: \xc3\x84\xc3\x96\xc3\x9c', '/home/galaxy/WMGalaxy/galaxy-dist/database/files/000/dataset_197.dat']) ('ascii' codec can't decode byte 0xc3 in position 22: ordinal not in range(128))

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