# HG changeset patch
# User devteam
# Date 1418155498 18000
# Node ID db10554eaad9b0c112b52c0c8519b5fc0dc54133
Uploaded
diff -r 000000000000 -r db10554eaad9 bamtools-filter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bamtools-filter.xml Tue Dec 09 15:04:58 2014 -0500
@@ -0,0 +1,331 @@
+
+ BAM datasets on a variety of attributes
+
+ bamtools
+
+
+
+ cat $script_file > $out_file2;
+
+ #for $bam_count, $input_bam in enumerate( $input_bams ):
+ ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &&
+ ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&
+ #end for
+
+ bamtools
+ filter
+ -script $script_file
+
+ #for $bam_count, $input_bam in enumerate( $input_bams ):
+ -in "localbam_${bam_count}.bam"
+ #end for
+ -out $out_file1
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+ ##Sets up a json configfile for bamtools filter
+ ##If there is more than one condition prints brackets and "filters:"
+ #if len( $conditions ) > 1
+ {
+ "filters":
+ [
+ #end if
+ #for $i, $c in enumerate( $conditions, start=1 )
+ { "id": "$i",
+ #for $j, $s in enumerate( $c.filters, start=1 )
+ ##The if below takes care of the comma at the end of last condition within group
+ #if $j != len( $c.filters)
+ "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}",
+ #else
+ "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}"
+ #end if
+ #end for
+ ##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
+ ]
+ #end if
+ }
+ #end if
+
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+**What is does**
+
+BAMTools filter is a very powerful utility to perform complex filtering of BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).
+
+-----
+
+**How it works**
+
+The tool use logic relies on the three concepts: (1) input BAM, (2) groups, and (3) filters.
+
+*Input BAM(s)*
+
+The input BAM is self-explanatory. This is the dataset you will be filtering. The tool can accept just one or multiple BAM files. To filter on multiple BAMs just add them by clicking **Add new BAM dataset(s) to filter**
+
+*Conditions and Filters*
+
+Conditions for filtering BAM files can be arranged in **Groups and Filters**. While it can be confusing at first this is what gives ultimate power to this tools. So try to look at the examples we are supplying below.
+
+-----
+
+**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.
+
+-----
+
+**Example 3. Complex filtering with multiple conditions**
+
+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**
+
+In the above example we have used two conditions (Condition 1 and Condition 2). Using multiple conditions allows to combine them and a variety of ways to enable even more powerful filtering.
+For example, suppose get all reads that (**1**) do NOT map to mitochondria and either (**2**) have mapping quality over 20, or (**3**) are in properly mapped pairs. The logical rule to enable such
+filtering will look like this::
+
+ !(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)
+
+-----
+
+**JSON script file**
+
+This tool produces two outputs. One of the them is a BAM file containing filtered reads. The other is a JSONified script. It can help you to see how your instructions are sent to BAMTools.
+For instance, the example 4 looks like this in the JSON form::
+
+ {
+ "filters":
+ [
+ { "id": "1",
+ "tag":"NM:=0",
+ "isReverseStrand":"false"
+ },
+ { "id": "2",
+ "tag":"NM:>0",
+ "isReverseStrand":"true"
+ }
+ ]
+ }
+
+
+
+-----
+
+**More information**
+
+.. class:: infomark
+
+Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
+
+
+
+
+ 10.1093/bioinformatics/btr174
+
+
diff -r 000000000000 -r db10554eaad9 images/complex-filters.png
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diff -r 000000000000 -r db10554eaad9 images/multiple-filters.png
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diff -r 000000000000 -r db10554eaad9 images/rule.png
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diff -r 000000000000 -r db10554eaad9 images/single-filter.png
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diff -r 000000000000 -r db10554eaad9 test-data/bamtools-input1.bam
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diff -r 000000000000 -r db10554eaad9 test-data/bamtools-test1.bam
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diff -r 000000000000 -r db10554eaad9 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Dec 09 15:04:58 2014 -0500
@@ -0,0 +1,6 @@
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