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clarify selection options
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docs/looper/advanced-guide/advanced-run-options.md

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@@ -244,24 +244,29 @@ Keys in the `cli.<subcommand>` section *must* match the long argument parser opt
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Looper provides several ways to select (filter) samples, so you only submit certain ones.
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### Sample selection
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### Sample selection by inclusion
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You can use `--sel-incl` with `--sel-attr`. You choose the attribute you want you want to select using, with `--sel-attr`. Then, you choose which values you want to include, with ``--sel-incl`.
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For example,
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To submit only certain samples, specify the sample attribute with `--sel-attr` and the values the attribute can take `--sel-incl`.
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For example, to choose only samples where the `species` attribute is `human`, `mouse`, or `fly`:
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```console
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looper run \
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--sel-attr species
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--sel-incl human mouse fly
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```
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This command would only run jobs for samples that have `human`, `mouse`, or `fly` as the value of the `species` attribute.
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Similarly, to submit only one sample, with `sample_name` as `sample`, you could use:
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```console
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looper run \
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--sel-attr sample_name
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--sel-incl sample1
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```
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### Sample exclusion
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### Sample selection by exclusion
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If more convenient to *exclude* samples by filter, you can use the analogous arguments `--sel-attr` with `--sel-excl`.
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This will
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### Toggling sample jobs through the sample table
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