<tool id="bwameth_index_builder_data_manager" name="bwa-meth index" tool_type="manage_data" version="1.0.0.1">
    <description>builder</description>
    <macros>
        <token name="@TOOL_VERSION@">0.2.2</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">bwameth</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
#if str($sequence_id).strip():
    #set $dbkey = $sequence_id
#else:
    #set $dbkey = $all_fasta_source.fields.dbkey
#end if

#if str($sequence_name).strip():
    #set $name = $sequence_name
#else:
    #set $name = $all_fasta_source.fields.name
#end if

python '$__tool_directory__/bwameth_index_builder.py' --output '${out_file}'
--fasta_filename '${all_fasta_source.fields.path}'
--dbkey '${dbkey}'
--name '${name}'
--data_table_name bwameth_indexes
    ]]></command>
    <inputs>
        <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
            <options from_data_table="all_fasta" />
        </param>
        <param name="sequence_id" type="text" value="" label="ID for index" help="If not specified, the value from the fasta file is used"/>
        <param name="sequence_name" type="text" value="" label="Displayed description for sequence" help="If not specified, the value from the fasta file is used"/>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <help><![CDATA[
.. class:: infomark

**Notice:** If you leave name, description, or id blank, it will be generated automatically.

What is BWA-meth?
-----------------

BWA-meth performs alignment of reads in a bisulfite-sequencing experiment (e.g., RRBS or WGBS) to a genome. The methodology employed for this is similar to bismark, where both the reads and the reference genome are *in silico* converted prior to alignment. Methylation extraction on the resulting BAM file can be done with the PileOMeth tool.

    ]]></help>
    <citations>
        <citation type="bibtex">@misc{1401.1129,
        Author = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz},
        Title = {Fast and accurate alignment of long bisulfite-seq reads},
        Year = {2014},
        Eprint = {arXiv:1401.1129},
        }</citation>
    </citations>
</tool>