galaxyproject / planemo

Command-line utilities to assist in developing Galaxy and Common Workflow Language artifacts - including tools, workflows, and training materials.
https://planemo.readthedocs.io/
MIT License
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revise seqtk boolean parameter example not to use shift quality #252

Open peterjc opened 9 years ago

peterjc commented 9 years ago

Currently docs/_writing_parameters.rst uses this as a boolean parameter example:

-V        shift quality by '(-Q) - 33'

This seems inappropriate and rather than exposing it as a user setting it should be automatic conditional on the datatype (i.e. use this for fastqillumina only). This could be used in a more complex example using conditionals in the Cheetah command tag and multiple input types.

I would suggest we replace the boolean parameter -V example with something simpler like -C or -N:

-C        drop comments at the header lines
-N        drop sequences containing ambiguous bases
hexylena commented 9 years ago

xref https://github.com/galaxyproject/tools-iuc/issues/204

bgruening commented 7 years ago

ping @martenson Fix was here: https://github.com/galaxyproject/tools-iuc/commit/f987b452b29c8b13181c7093c077e2612dd1ac1b