Add a --smartLabels option, to auto strip path and file extension in labels.

[dpryan79]

This was requested internally and I'd be surprised if others wouldn't like it too. Provided your file names are otherwise meaningful you could use this such that -b path/foo1.bam path2/foo2.bam had labelsfoo1 and foo2, which would be convenient with large numbers of samples where it's annoying to manually set these (yes, one could do this in snakemake, but for one-off stuff this is simpler).

This wouldn't be needed in Galaxy.

[dpryan79]

Note that this option won't be exposed in Galaxy, since it wouldn't make sense there.

[dpryan79]

The following have been tested

• computeMatrix (this was already secretly doing that)
• estimateReadFiltering
• multiBamSummary
• multiBigwigSummary
• plotCoverage
• plotEnrichment
• plotFingerprint

computeMatrix, plotEnrichment, and the multi*Summary programs can take BED files as well. I need to check exactly what will happen if I use --smartLabels with them while also specifying a label inside the file (likewise, what happens with GTF files?). I think the smart label becomes the default and is simply overridden, but this needs to be confirmed.

[dpryan79]

As an aside, I see that some of the plot* functions already strip the path if you don't specify a label. It would have been nice if that were documented.

[dpryan79]

This is now implemented in develop.

[kelly-sovacool]

FYI this option appears to be missing from the docs: https://deeptools.readthedocs.io/en/develop/index.html