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docuemntation update
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bedroesb committed Jan 18, 2022
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Expand Up @@ -165,7 +165,7 @@ Use the *--dev* flag if you want to do a test submission using the tool by the s
There are two ways of submitting only a selection of objects to ENA. This is handy for reoccurring submissions, especially when they belong to the same study.

- Manual: you can add an optional `status` column to every table/sheet that contains the action you want to apply during this submission. If you chose to add only the first 2 samples to ENA, you specify `--action add` as parameter in the command and you add the `add` value to the status column of the rows you want to submit as demonstrated below. Same holds for the action `modify`, `release` and `cancel`.
- Automatic (BETA): using the `--auto_action` it is possible to auto detect wether an object (using the alias) is already present on ENA and will add `modify` or `add` to the table. This works only with ENA objects that are published and findable on the website trough the search function. If the tool does not correctly detect its presence on the website we suggest to use the more robust manual approach as discribed above.
- Automatic (BETA): using the `--auto_action` it is possible to auto detect wether an object (using the alias) is already present on ENA and will fill in the specified action (`--action` parameter) accordingly. In practice, this means that if a user chooses to add objects and we already find this object already exists using its alias, this objects will not be added. On the other hand, if the command is used to modify objects, we want to apply this solely on objects that already exist on ENA. The detection only works with ENA objects that are published and findable on the website trough the search function (both the dev and live website). If the tool does not correctly detect the presence of your ENA object, we suggest to use the more robust manual approach as described above.

**Example with modify as seen in the [example sample modify table](example_tables/ENA_template_samples_modify.tsv)**

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