make ThermoRawFileParser run parallel

[bernt-matthias]

and

• add stdio (script returns always exit code 0)
• fix citation

fixes #558
should fix #557

we could also use the opportunity and update to 1.3.2 ... but I do not have the time to bump the bioconda recipe.

[martenson]

We could postpone merging this after bioconda/bioconda-recipes#26729 - the bioconda build is passing now.

[bernt-matthias]

Yep. Lets do this. Can you check here https://github.com/compomics/ThermoRawFileParser/blob/master/README.md if there are new parameters that we should add?

[martenson]

Maybe the exception data?

--- from_file
+++ ThermoRawFileParser.exe --help
@@ -28,10 +28,17 @@
   -z, --noZlibCompression    Don't use zlib compression for the m/z ratios and
                                intensities. By default zlib compression is
                                enabled.
+  -a, --allDetectors         Extract additional detector data: UV/PDA etc
   -l, --logging=VALUE        Optional logging level: 0 for silent, 1 for
                                verbose.
   -e, --ignoreInstrumentErrors
                              Ignore missing properties by the instrument.
+  -x, --includeExceptionData Include reference and exception data
+  -L, --msLevel=VALUE        Select MS levels (MS1, MS2, etc) included in the
+                               output, should be a comma-separated list of
+                               integers ( 1,2,3 ) and/or intervals ( 1-3 ),
+                               open-end intervals ( 1- ) are allowed
+  -P, --mgfPrecursor         Include precursor scan number in MGF file TITLE
   -u, --s3_url[=VALUE]       Optional property to write directly the data into
                                S3 Storage.
   -k, --s3_accesskeyid[=VALUE]

[martenson]

1.3.2 is ready https://anaconda.org/bioconda/thermorawfileparser/files

[bernt-matthias]

@martenson the last test should fail (parquet generation) .. and succeed with bioconda/bioconda-recipes#26756 (I tested this manually as described here https://planemo.readthedocs.io/en/latest/writing_how_do_i.html#test-tools-against-a-package-or-container-in-a-bioconda-pull-request)

[bernt-matthias]

Tests do not run at all since we need release_21.01 (for parquet) which would come with #561

But we can discuss if we want such a recent profile or if its preferable to omit parquet for now.

Also I'm not 100% sure about the output format specific options which I implemented in the conditional.

[martenson]

The tools/ThermoRawFileParser/test-data/really_small.parquet file displays as having 0 bytes to me.

[bgruening]

I'm wondering what this implies? Is there a use-case for our users to disable it?

[bernt-matthias]

As far as I know different compression schemes can be used for numerical values. Maybe one or the other downstream tool is incompatible with the default ..

[martenson]

Thanks a lot @bernt-matthias! And for the review @bgruening 👍