Hi all,

I think I've found a bug in the Galaxy test framework :(

With most file inputs, a gzipped input file works fine (Galaxy's upload code
handles unzipping it). However, with multiple="true" this seems to break
(with the Twill backend, the API test framework is OK), e.g.

<param name="filenames" type="data" format="fastq,mira"
multiple="true" required="true" label="Read file(s)"
                  help="Multiple files allowed, for example paired
reads can be given as two files (MIRA looks at read names to identify
pairs)." />


Fails:

<param name="filenames" value="SRR639755_mito_pairs_sample.fastq.gz"
ftype="fastqsanger" />

e.g.  https://travis-ci.org/peterjc/pico_galaxy/builds/27426318

Excerpt from log:

======================================================================
FAIL: test_tool_000000 (functional.test_toolbox.TestForTool_mira_4_0_de_novo)
MIRA v4.0 de novo assember ( mira_4_0_de_novo ) > Test-1
----------------------------------------------------------------------
Traceback (most recent call last):
File 
"/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/functional/test_toolbox.py",
line 108, in test_tool
self.do_it( td )
File 
"/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/functional/test_toolbox.py",
line 32, in do_it
data_list = galaxy_interactor.run_tool( testdef, test_history )
File 
"/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/interactor.py",
line 449, in run_tool
self.twill_test_case.run_tool( testdef.tool.id,
repeat_name=repeat_name, **page_inputs )
File 
"/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/twilltestcase.py",
line 1789, in run_tool
self.submit_form( **kwd )
File 
"/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/twilltestcase.py",
line 1999, in submit_form
raise AssertionError( errmsg )
AssertionError: Attempting to set field 'read_group_0|filenames' to
value '['SRR639755_mito_pairs_sample.fastq.gz']' in form 'tool_form'
threw exception: id=None name=None
label='SRR639755_mito_pairs_sample.fastq.gz'
control: <SelectControl(read_group_0|filenames=[80])>
If the above control is a DataToolparameter whose data type class does
not include a sniff() method,
make sure to include a proper 'ftype' attribute to the tag for the
control within the <test> tag set.


This works,

<param name="filenames" value="SRR639755_mito_pairs_sample.fastq"
ftype="fastqsanger" />

e.g. https://travis-ci.org/peterjc/pico_galaxy/builds/27426336

See: 
https://github.com/peterjc/pico_galaxy/commit/e6967767535ca29debcdc19d7f0502d73276b6a0

Regards,

Peter
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