comparison bamtools-filter.xml @ 4:baca6d3e27af draft

planemo upload commit 5ad726dc73203a704666033cd3bf70b82575978f-dirty

3:07d099ccd10f

**Example 1. Using a single filter**

When filtering on a single condition there is no need to worry about filters and conditions. Just choose a filter from the **Select BAM property to filter on:** dropdown and enter a value (or click a checkbox for binary filters).
For example, for retaining reads with mapping quality of at least 20 one would set the tool interface as shown below:

.. image:: ${static_path}images/single-filter.png

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**Example 2. Using multiple filters**

Now suppose one needs to extract reads that (1) have mapping quality of at least 20, (2) contain at least 1 mismatch, and (3) are mapping onto forward strand only.
To do so we will use three filters as shown below (multiple filters are added to the interface by clicking on the **Add new Filter** button):

.. image:: ${static_path}images/multiple-filters.png

In this case (you can see that the three filters are grouped within a single Condition - **Condition 1**) the filter too use logical **AND** to perform filtering.
In other words only reads that (1) have mapping quality of at least 20 **AND** (2) contain at least 1 mismatch **AND** are mapping onto forward strand will be returned in this example.

-----

Suppose now you would like to select **either** reads that (**1**) have (*1.1*) no mismatches and (*1.2*) are on the forward strand **OR** (**2**) reads that have (*2.1*) 
at least one mismatch and (*2.2*) are on the reverse strand. In this scenario we have to set up two conditions: (**1**) and (**2**) each with two filters: *1.1* and *1.2* as well as *2.1* and *2.2*. 
The following screenshot expalins how this can be done:

.. image:: ${static_path}images/complex-filters.png

-----

**Example 4. Even more complex filtering with Rules**

 !(1) & (2 | 3)
 
Here, numbers 1, 2, and 3 represent conditions. The following screenshot illustrates how to do this in Galaxy:

.. image:: ${static_path}images/rule.png

There are three conditions here, each with a single filter. A text entry area that can be opened by clicking on the **Would you like to set rules?** checkbox enables you to enter a rule.
Here numbers correspond to numbers of conditions as they are shown in the interface. E.g., 1 corresponds to condition 1, 2 to condition 2 and so on... In human language this means::

 NOT condition 1 AND (condition 2 OR condition 3)

4:baca6d3e27af

**Example 1. Using a single filter**

When filtering on a single condition there is no need to worry about filters and conditions. Just choose a filter from the **Select BAM property to filter on:** dropdown and enter a value (or click a checkbox for binary filters).
For example, for retaining reads with mapping quality of at least 20 one would set the tool interface as shown below:

.. image:: ${static_path}/single-filter.png

-----

**Example 2. Using multiple filters**

Now suppose one needs to extract reads that (1) have mapping quality of at least 20, (2) contain at least 1 mismatch, and (3) are mapping onto forward strand only.
To do so we will use three filters as shown below (multiple filters are added to the interface by clicking on the **Add new Filter** button):

.. image:: ${static_path}/multiple-filters.png

In this case (you can see that the three filters are grouped within a single Condition - **Condition 1**) the filter too use logical **AND** to perform filtering.
In other words only reads that (1) have mapping quality of at least 20 **AND** (2) contain at least 1 mismatch **AND** are mapping onto forward strand will be returned in this example.

-----

Suppose now you would like to select **either** reads that (**1**) have (*1.1*) no mismatches and (*1.2*) are on the forward strand **OR** (**2**) reads that have (*2.1*) 
at least one mismatch and (*2.2*) are on the reverse strand. In this scenario we have to set up two conditions: (**1**) and (**2**) each with two filters: *1.1* and *1.2* as well as *2.1* and *2.2*. 
The following screenshot expalins how this can be done:

.. image:: ${static_path}/complex-filters.png

-----

**Example 4. Even more complex filtering with Rules**

 !(1) & (2 | 3)
 
Here, numbers 1, 2, and 3 represent conditions. The following screenshot illustrates how to do this in Galaxy:

.. image:: ${static_path}/rule.png

There are three conditions here, each with a single filter. A text entry area that can be opened by clicking on the **Would you like to set rules?** checkbox enables you to enter a rule.
Here numbers correspond to numbers of conditions as they are shown in the interface. E.g., 1 corresponds to condition 1, 2 to condition 2 and so on... In human language this means::

 NOT condition 1 AND (condition 2 OR condition 3)