comparison bamtools-filter.xml @ 9:c20a4a4acf3f draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b

8:709d8669e8d6

<tool id="bamFilter" name="Filter" version="0.0.1">
  <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
    
    bamtools
    filter
    -script $script_file
    
    #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">
      <repeat name="filters" title="Filter" min="1">
        <conditional name="bam_property">
          <param name="bam_property_selector" type="select" label="Select BAM property to filter on">
            <option value="alignmentFlag"/>

        [
      #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

    <data format="txt" name="out_file2" />
    <data format="bam" name="out_file1" />
  </outputs>
    <tests>
        <test>
            <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
            <param name="bam_property_selector" value="mapQuality"/>
            <param name="bam_property_value" value=">20"/>
            <output name="out_file1" file="bamtools-test1.bam" ftype="bam"/>        
        </test>
    </tests>
<help>
**What is does**

-----

**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:: complex-filters.png

-----

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:: 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.

9:c20a4a4acf3f

<tool id="bamFilter" name="Filter" version="0.0.2">
  <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}" "localbam_${bam_count}.bam" &amp;&amp;
      ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp;
    #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
  </command>
  <inputs>
    <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/>
    <repeat name="conditions" title="Condition" min="1">
      <repeat name="filters" title="Filter" min="1">
        <conditional name="bam_property">
          <param name="bam_property_selector" type="select" label="Select BAM property to filter on">
            <option value="alignmentFlag"/>

        [
      #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

    <data format="txt" name="out_file2" />
    <data format="bam" name="out_file1" />
  </outputs>
    <tests>
        <test>
            <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
            <param name="bam_property_selector" value="mapQuality"/>
            <param name="bam_property_value" value=">20"/>
            <output name="out_file1" file="bamtools-test1.bam" ftype="bam"/>
        </test>
    </tests>
<help>
**What is does**

-----

**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:: complex-filters.png

-----

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:: 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.