comparison bamtools-filter.xml @ 1:5e2fe70292a7 draft

planemo upload commit 5ad726dc73203a704666033cd3bf70b82575978f-dirty

0:db10554eaad9

  <description>BAM datasets on a variety of attributes</description>
  <requirements>
    <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement>
  </requirements>
  <command>

    cat $script_file > $out_file2;
    
    #for $bam_count, $input_bam in enumerate( $input_bams ):
        ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &amp;&amp;
        ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp;
    #end for
    

    
    #for $bam_count, $input_bam in enumerate( $input_bams ):
        -in "localbam_${bam_count}.bam"
    #end for
    -out $out_file1
    
  </command>

  <inputs>
    <repeat name="input_bams" title="BAM dataset(s) to filter" min="1">
          <param name="input_bam" type="data" format="bam" label="BAM dataset" />
    </repeat>
    <repeat name="conditions" title="Condition" min="1">

          ##The if below takes care of the comma at the end of last condition within group 
          #if $i != len( $conditions )
          },
          #else
          }
          #end if      
      #end for   
      #if len( $conditions ) > 1
      #if str( $rule_configuration.rules_selector ) == "True":
        ],
          "rule" : "${rule_configuration.rules}"
        #else

**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/simple-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}/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)

            "tag":"NM:>0",
            "isReverseStrand":"true"
          }
        ]
      }
    
    

-----

**More information**

1:5e2fe70292a7

  <description>BAM datasets on a variety of attributes</description>
  <requirements>
    <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement>
  </requirements>
  <command>
    cat $script_file > $out_file2;

    #for $bam_count, $input_bam in enumerate( $input_bams ):
        ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &amp;&amp;
        ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp;
    #end for
    

    
    #for $bam_count, $input_bam in enumerate( $input_bams ):
        -in "localbam_${bam_count}.bam"
    #end for
    -out $out_file1
  </command>
  <inputs>
    <repeat name="input_bams" title="BAM dataset(s) to filter" min="1">
          <param name="input_bam" type="data" format="bam" label="BAM dataset" />
    </repeat>
    <repeat name="conditions" title="Condition" min="1">

          ##The if below takes care of the comma at the end of last condition within group 
          #if $i != len( $conditions )
          },
          #else
          }
          #end if
      #end for
      #if len( $conditions ) > 1
      #if str( $rule_configuration.rules_selector ) == "True":
        ],
          "rule" : "${rule_configuration.rules}"
        #else

**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:: images/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:: 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:: 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:: 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)

            "tag":"NM:>0",
            "isReverseStrand":"true"
          }
        ]
      }


-----

**More information**