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formatting fixes to README
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will-moore committed Jul 10, 2019
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22 changes: 11 additions & 11 deletions README.rst
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Expand Up @@ -40,8 +40,8 @@ The plugin is called from the command-line using the `omero` command::
$ bin/omero metadata <subcommand>

Help for each command can be shown using the ``-h`` flag.
Objects can be specified as arguments in the format ```Class:ID```, such
as ```Project:123```.
Objects can be specified as arguments in the format ``Class:ID``, such
as ``Project:123``.

Available subcommands are:

Expand Down Expand Up @@ -72,11 +72,11 @@ If you wish to ensure that ``number`` columns are created for numerical data, th
allow you to make numerical queries on the table.
Column Types are:

- 'plate', 'well', 'image', 'dataset', 'roi' to specify objects
- 'd': DoubleColumn, for floating point numbers
- 'l': LongColumn, for integer numbers
- 's': StringColumn, for text
- 'b': BoolColumn, for true/false
- ``d``: ``DoubleColumn``, for floating point numbers
- ``l``: ``LongColumn``, for integer numbers
- ``s``: ``StringColumn``, for text
- ``b``: ``BoolColumn``, for true/false
- ``plate``, ``well``, ``image``, ``dataset``, ``roi`` to specify objects

These can be specified in the first row of a ``CSV`` with a ``# header`` tag (see examples below).
The ``# header`` row is optional. Default column type is ``String``.
Expand All @@ -87,7 +87,7 @@ by these columns.
Examples:

To add a table to a Project, the ``CSV`` file needs to specify ``Dataset Name``
and ``Image Name``:
and ``Image Name``::

$ bin/omero metadata populate Project:1 path/to/project.csv

Expand All @@ -114,7 +114,7 @@ img-04.png dataset01 0.429 4 Cy5 36641
If the target is a Dataset instead of a Project, the ``Dataset Name`` column is not needed.

To add a table to a Screen, the ``CSV`` file needs to specify ``Plate`` name and ``Well``.
If a ```# header``` is specified, column types must be ``well`` and ``plate``.
If a ``# header`` is specified, column types must be ``well`` and ``plate``.

screen.csv::

Expand All @@ -126,8 +126,8 @@ screen.csv::
B1,plate01,DrugX,12.3,50,44.43

This will create an OMERO.table linked to the Screen, with the
```Well Name``` and ```Plate Name``` columns added and the ```Well``` and
```Plate``` columns used for IDs:
``Well Name`` and ``Plate Name`` columns added and the ``Well`` and
``Plate`` columns used for IDs:

===== ====== ====== ============== =========== ================ =========== ===========
Well Plate Drug Concentration Cell_Count Percent_Mitotic Well Name Plate Name
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