gffcompare: fix for creating extra files in database/files/

[bernt-matthias]

gffcompare creates extra files in the basedir of the input files. This leads to an error when jobs run as real user and is unwanted anyway.

For instance, for the input database/files/001/295/dataset_1295486.dat the files

• database/files/001/295/gffcmp.dataset_1295486.dat.tmap
• database/files/001/295/gffcmp.dataset_1295486.dat.tloc

would be created.

My solution is to create links, since this offers the possibility to add these files to an output collection. Alternatively with -T the creation could be forbidden.

General question: would it be a good idea to link all input data to the working directory by default?

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[bernt-matthias]

This should be nearly it:

• also fixed wrong filter statements for the annotated and combined outputs

Tests are not working for me locally: Exception: Incorrect number of outputs - expected 6, found 4. and Exception: Incorrect number of outputs - expected 4, found 5.

When I try manually (planemo s) the number or outputs is correct. Also the tests without expect_num_outputs work.

[bernt-matthias]

Anyone has an idea why the number of outputs seems to be wrong. For me the planemo tests seem to be correct. Do I count wrong or is planemo?

[mblue9]

@bernt-matthias the collection outputs don't get counted by planemo (don't know why) so the first test should be just 4 expect_num_outputs="4".

Don't know why the second test is counting 5 as looks like should be 4 to me.

[bernt-matthias]

Tests work now against this: galaxyproject/galaxy#6931

Indeed galaxy counted wrong.

Additionally the number of gffinputs is a list of HDAs in case of multiple inputs and a single HDA otherwise. Which is why the filters previously did not work.

[bernt-matthias]

Something is odd with the testing. The errors are related to different tools. Any ideas.

The tests of the tools should work now, since galaxyproject/galaxy#6931 was just merged into dev.

[nsoranzo]

Something is odd with the testing. The errors are related to different tools. Any ideas.

@bernt-matthias See #2160

The tests of the tools should work now, since galaxyproject/galaxy#6931 was just merged into dev.

We use release_18.09 at the moment, not dev, see .travis.yml

[nsoranzo]

@bernt-matthias The linting issue has been fixed. Now the first test fails with "Exception: Incorrect number of outputs - expected 6, found 4." because your fix is only in Galaxy dev, do you want to backport it to 18.09?

[bernt-matthias]

@nsoranzo galaxyproject/galaxy#6951

[bernt-matthias]

hooray. all tests passed after galaxyproject/galaxy#6951 was merged.