Hi Peter,

What is the test error given when you do have a value defined for name in 
output?


Can you try using 'empty_file.dat'?

e.g.

       <output name="out_file" file="empty_file.dat" >

or

        <output name="out_file" file="empty_file.dat" compare="contains">

etc




Thanks for using Galaxy,


Dan


On Apr 4, 2013, at 1:34 PM, Peter Cock wrote:

> On Wed, Apr 3, 2013 at 2:48 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> On Wed, Apr 3, 2013 at 2:37 PM, Dave Bouvier <d...@bx.psu.edu> wrote:
>>> For the outputs, rgClean.xml provides an example of comparing a
>>> composite output dataset with the expected test data.
>> 
>> Here there is a tag <extra_files> used within the <output> tag.
>> 
>> Many thanks Dave - those should be enough to get me started, and
>> maybe I can update the wiki once I'm happy with how this works...
> 
> I'm trying this for makeblastdb which produces a single output,
> a composite datatype which is a BLAST database.
> 
> The examples I found all seemed to be composite datatypes with
> a central file (e.g. HTML plus images), i.e.
> composite_type='auto_primary_file'
> 
> In the case of the BLAST databases, this is a composite datatype
> without a primary file, aka composite_type='basic'. Leaving the
> <param> without a file gives:
> 
> Exception: Test output does not have a 'file'
> 
> Using a empty value doesn't work,
> 
> Traceback (most recent call last):
>  File "/mnt/galaxy/galaxy-central/test/functional/test_toolbox.py",
> line 171, in test_tool
>    self.do_it( td, shed_tool_id=shed_tool_id )
>  File "/mnt/galaxy/galaxy-central/test/functional/test_toolbox.py",
> line 102, in do_it
>    self.verify_dataset_correctness( outfile, hid=elem_hid,
> maxseconds=testdef.maxseconds, attributes=attributes,
> shed_tool_id=shed_tool_id )
>  File "/mnt/galaxy/galaxy-central/test/base/twilltestcase.py", line
> 828, in verify_dataset_correctness
>    self.files_diff( local_name, temp_name, attributes=attributes )
>  File "/mnt/galaxy/galaxy-central/test/base/twilltestcase.py", line
> 66, in files_diff
>    local_file = open( file1, 'U' ).readlines()
> IOError: [Errno 21] Is a directory: '/mnt/galaxy/galaxy-central/test-data'
> 
> Using /dev/null gets a bit further but something is confusing the
> comparisons.
> 
> My current experimental test looks like this:
> 
> <tests>
>    <test>
>        <param name="dbtype" value="prot"/>
>        <param name="file" value="four_human_proteins.fasta"/>
>        <param name="title" value="Just 4 human proteins"/>
>        <param name="parse_seqids" value=""/>
>        <param name="hash_index" value="-hash_index"/>
>        <output name="out_file" file="/dev/null" ftype="blastdbp">
>            <extra_files type="file"
> value="four_human_proteins.fasta.phd" name="blastdb.pdb"/>
>            <extra_files type="file"
> value="four_human_proteins.fasta.phi" name="blastdb.phi"/>
>            <extra_files type="file"
> value="four_human_proteins.fasta.phr" name="blastdb.phr"/>
>            <extra_files type="file"
> value="four_human_proteins.fasta.pin" name="blastdb.pin"/>
>            <extra_files type="file"
> value="four_human_proteins.fasta.pog" name="blastdb.pog"/>
>            <extra_files type="file"
> value="four_human_proteins.fasta.psd" name="blastdb.psd"/>
>            <extra_files type="file"
> value="four_human_proteins.fasta.psi" name="blastdb.psi"/>
>            <extra_files type="file"
> value="four_human_proteins.fasta.psq" name="blastdb.psq"/>
>        </output>
>    </test>
> </tests>
> 
> Any advice?
> 
> Thanks,
> 
> Peter
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