<tool id="bwameth_index_builder_data_manager" name="bwa-meth index" tool_type="manage_data" version="1.0.0">
    <description>builder</description>
    <requirements>
        <requirement type="package" version="0.7.12">bwa</requirement>
        <requirement type="package" version="1.2">samtools</requirement>
        <requirement type="package" version="0.2.0">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 label="Source FASTA Sequence" name="all_fasta_source" type="select">
            <options from_data_table="all_fasta" />
        </param>
        <param label="ID for index" name="sequence_id" type="text" value="" help="If not specified, the value from the fasta file is used"/>
        <param label="Displayed description for sequence" name="sequence_name" type="text" value="" help="If not specified, the value from the fasta file is used"/>
    </inputs>
    <outputs>
        <data format="data_manager_json" name="out_file" />
    </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>