diff --git a/docs/usage/cli/filter.rst b/docs/usage/cli/filter.rst index 8923b0d42..fa47f6dda 100644 --- a/docs/usage/cli/filter.rst +++ b/docs/usage/cli/filter.rst @@ -36,7 +36,7 @@ A simple example use of this command would be This command will select all sequences with collection date in 2012 or later. The filter command has a large number of options that allow flexible filtering for many common situations. One such use-case is the exclusion of sequences that are known to be outliers (e.g. because of sequencing errors, cell-culture adaptation, ...). -These can be specified in a separate file: +These can be specified in a separate text file (e.g. ``exclude.txt``): .. code-block:: @@ -44,7 +44,7 @@ These can be specified in a separate file: COL/FLR_00034/2015 ... -To drop such strains, you can use ``--exclude``: +To drop such strains, you can pass the filename to ``--exclude``: .. code-block:: bash @@ -52,7 +52,7 @@ To drop such strains, you can use ``--exclude``: --sequences data/sequences.fasta \ --metadata data/metadata.tsv \ --min-date 2012 \ - --exclude config/dropped_strains.txt \ + --exclude exclude.txt \ --output-sequences filtered_sequences.fasta \ --output-metadata filtered_metadata.tsv