On Wed, Apr 3, 2013 at 2:48 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Wed, Apr 3, 2013 at 2:37 PM, Dave Bouvier <dave@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