Fix `pysam.index()` calls which now use samtools 1.16 where
`samtools index input output` doesn't work any more if `output` is the path
of an already existing file, but `samtools index -o output input` works
fine.
Also:
- Pre-create the (empty) index file for mock test datasets as a unit test
reproducer of the above issue.
- Fix `test_cram` unit test that wasn't checking the return value of
`CRAM.set_index_file()`, which was in fact returning False because
`test-data/2.cram` was not sorted (updated now).
Somewhere between file/libmagic 5.36 and 5.39, the output of `file` on a
`.csi` file changed, breaking the ``metadata_bcf`` framework test with
the following error:
```
if found_exceptions:
> raise JobOutputsError(found_exceptions, job_stdio)
E galaxy.tool_util.verify.interactor.JobOutputsError: Output output_of_input_metadata: different than expected, difference (using contains):
E ( /tmp/tmpu1a3dgjcbcf_index_metadata_test.txt v. /tmp/tmpkt78tzggbcf_index_metadata_test.txt )
E Failed to find 'gzip compressed data, extra field' in history data. (lines_diff=0):
lib/galaxy/tool_util/verify/interactor.py:1222: JobOutputsError
```
So add a requirement for the latest `file` version and update the test
accordingly.
dont compare the json file content but rely completely on the assertions on
the loaded json contents.
the json content test was superficial and did not work anymore since the order
of the keys differed. it worked before since the inputs contained only a
single key.
- in particular the case of an empty select did yield "None" before
now its []
Problem was that the ValueWrapper is not None if nothing is selected
- but also non empty selects were "option1,option2" now its
["option1","option2"]
- renamed variable value -> value_wrapper
Demonstrates using the Apply Rules collection operation tool against existing collections to:
- Use grouping to build nested lists from flat ones.
- Invert nested collections.
- Filter collections.
- Filter while also grouping to build nested collections.
Based on count data used in the DESeq2 tutorial (http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html), originally from the Bioconductor Pasilla package (http://bioconductor.org/packages/release/data/experiment/html/pasilla.html). Citation: Huber W, Reyes A (2018). pasilla: Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011.. R package version 1.8.0.
Leonid Kostrykin