<tool id="add_matesequence" name="Add matesequence" version="0.3.9">
    <description>into tag field</description>
    <requirements>
        <requirement type="package" version="0.3.9">readtagger</requirement>
    </requirements>
    <version_command>add_matesequence --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
        add_matesequence --file_to_annotate '$file_to_annotate' --annotate_source '$annotate_source' --output_path '$output'
    ]]></command>
    <inputs>
        <param name="file_to_annotate" argument="--file_to_annotate" label="Annotate reads in this file with their mate sequence" type="data" format="bam"/>
        <param name="annotate_source" argument="--annotate_source" label="Use this file to find the mate sequence (can be same file as file_to_annotate)" type="data" format="bam"/>
        <param name="mate_sequence_tag" type="text" value="MS"/>
    </inputs>
    <outputs>
        <data name="output" format="bam" label="Add matesequence on $on_string"/>
    </outputs>
    <tests>
        <test>
            <param name="file_to_annotate" value="dm6.bam" ftype="bam"/>
            <param name="annotate_source" value="dm6.bam" ftype="bam"/>
            <output name="output" file="dm6_mate_annotated.bam" ftype="bam" lines_diff="2"/>
        </test>
    </tests>
    <help><![CDATA[
.. code-block::

    usage: add_matesequence [-h] -a FILE_TO_ANNOTATE -s ANNOTATE_SOURE -o
                            OUTPUT_PATH [--version]

    Annotate reads with Mate Sequence in tag field

    optional arguments:
      -h, --help            show this help message and exit
      -a FILE_TO_ANNOTATE, --file_to_annotate FILE_TO_ANNOTATE
                            Annotate reads in this file with their mate sequence
      -s ANNOTATE_SOURE, --annotate_soure ANNOTATE_SOURE
                            Use this file to find the mate sequence (can be same
                            file as file_to_annotate)
      -o OUTPUT_PATH, --output_path OUTPUT_PATH
                            Write resulting BAM file to this path
      --version             show program's version number and exit

    ]]></help>
</tool>