comparison bamtools-filter.xml @ 12:ce5482dfe8bd draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 08b8fbdbce3ec7ccc8eb93d8c6b7a5234459cca9

11:6fae66d050a7

<tool id="bamFilter" name="Filter" version="2.4.1">
    <description>BAM datasets on a variety of attributes</description>
    <requirements>
        <requirement type="package" version="2.4.0">bamtools</requirement>
    </requirements>
    <command>
        <![CDATA[
            cp '$script_file' '$out_file2' &&
            ln -s '${input_bam}' localbam.bam &&
            ln -s '${input_bam.metadata.bam_index}' localbam.bam.bai &&
            bamtools filter -script '$script_file' -in localbam.bam -out '$out_file1'

                    </when>
                    <when value="cigar">
                        <param name="bam_property_value" type="text" value="101M" label="Filter on this CIGAR string" help="Default (101M) is for 101 continuously matched bases"/>
                    </when>
                    <when value="insertSize">
                        <param name="bam_property_value" type="text" value=">=250" label="Filter on insert size" help="You can use &gt;, &lt;, =, and ! (not) in your expression. E.g., to select pairs with insert size above 250 nt use &quot;>=250&quot;">
                            <sanitizer invalid_char="">
                                <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/><add value="-"/></valid>
                            </sanitizer>
                        </param>
                    </when>

                    </when>
                    <when value="isSecondMate">
                        <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select second mate in a read pair" help="Checked = Read IS second mate, Empty = Read is NOT second mate"/>
                    </when>
                    <when value="mapQuality">
                        <param name="bam_property_value" type="text" value="20" label="Filter on read mapping quality (phred scale)" help="You can use &gt;, &lt;, =, and ! (not) in your expression. E.g., to select reads with mapping quality of at least 30 use &quot;>=30&quot;">
                            <sanitizer invalid_char="">
                                <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
                            </sanitizer>
                        </param>
                    </when>

                                <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
                            </sanitizer>
                        </param>
                    </when>
                    <when value="tag">
                        <param name="bam_property_value" type="text" value="NM:&gt;1" label="Filter on a particular tag" help="You can use &gt;, &lt;, =, and ! (not).  Tag name and its value must be separated by &quot;:&quot;. E.g., to obtain reads with at least one mismatch use &quot;NM:&gt;1&quot;">
                            <sanitizer invalid_char="">
                                <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value=":!="/></valid>
                            </sanitizer>
                        </param>
                    </when>
                </conditional>
            </repeat>

    </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" ftype="bam" file="bamtools-test1.bam" />
        </test>
    </tests>
    <help>
**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).

-----

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

**More information**

.. class:: infomark

Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki


    </help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btr174</citation>
    </citations>
</tool>

12:ce5482dfe8bd

<tool id="bamFilter" name="Filter" version="2.4.1">
    <description>BAM datasets on a variety of attributes</description>
    <macros>
          <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
        <![CDATA[
            cp '$script_file' '$out_file2' &&
            ln -s '${input_bam}' localbam.bam &&
            ln -s '${input_bam.metadata.bam_index}' localbam.bam.bai &&
            bamtools filter -script '$script_file' -in localbam.bam -out '$out_file1'

                    </when>
                    <when value="cigar">
                        <param name="bam_property_value" type="text" value="101M" label="Filter on this CIGAR string" help="Default (101M) is for 101 continuously matched bases"/>
                    </when>
                    <when value="insertSize">
                        <param name="bam_property_value" type="text" value="&gt;=250" label="Filter on insert size" help="You can use &gt;, &lt;, =, and ! (not) in your expression. E.g., to select pairs with insert size above 250 nt use &quot;&gt;=250&quot;">
                            <sanitizer invalid_char="">
                                <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/><add value="-"/></valid>
                            </sanitizer>
                        </param>
                    </when>

                    </when>
                    <when value="isSecondMate">
                        <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select second mate in a read pair" help="Checked = Read IS second mate, Empty = Read is NOT second mate"/>
                    </when>
                    <when value="mapQuality">
                        <param name="bam_property_value" type="text" value="20" label="Filter on read mapping quality (phred scale)" help="You can use &gt;, &lt;, =, and ! (not) in your expression. E.g., to select reads with mapping quality of at least 30 use &quot;&gt;=30&quot;">
                            <sanitizer invalid_char="">
                                <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
                            </sanitizer>
                        </param>
                    </when>

                                <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
                            </sanitizer>
                        </param>
                    </when>
                    <when value="tag">
                        <param name="bam_property_value" type="text" value="NM:&gt;1" label="Filter on a particular tag" help="You can use +, -, &gt;, &lt;, =, and ! (not).  Tag name and its value must be separated by &quot;:&quot;. E.g., to obtain reads with at least one mismatch use &quot;NM:&gt;1&quot;">
                            <sanitizer invalid_char="">
                                <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value=":!=+-"/></valid>
                            </sanitizer>
                        </param>
                    </when>
                </conditional>
            </repeat>

    </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="&gt;20"/>
            <output name="out_file1" ftype="bam" file="bamtools-test1.bam" />
        </test>
    </tests>
    <help>
<![CDATA[
**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).

-----

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

**More information**

.. class:: infomark

Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
]]>
    </help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btr174</citation>
    </citations>
</tool>