galaxyproject / galaxyproject/planemo

revise seqtk boolean parameter example not to use shift quality

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#252 2 comments 0 reactions 1 assignee Claimed by @martenson View on GitHub
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Python
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Description

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
```

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