<macros>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/bioinformatics/btu138</citation>
            <yield />
        </citations>
    </xml>
    
    <xml name="requirements">
        <requirements>
              <requirement type="package" version="0.5.4">presto</requirement>
        </requirements>
    </xml>
    
    <xml name="presto-coord-param">
        <param argument="--coord" type="select"  value="presto"  label="Coordinate" help="The format of the sequence identifier which defines shared coordinate information across mate pairs.">
            <option value="illumina">Illumina</option>
            <option value="solexa">Solexa</option>
            <option value="sra">SRA</option>
            <option value="454">454</option>
            <option value="presto">pRESTO</option>
        </param>
    </xml>
    
    <xml name="presto-log-param">
        <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/>
    </xml>
    
    <xml name="presto-log-output">
        <data name="log_out" format="txt" label="Log from ${tool.name} on ${on_string}">
            <filter>capture_log</filter>
        </data>
    </xml>
    
    <xml name="text-regex-validator">
        <validator type="regex" message="Value may include alphanumeric characters, underscores and spaces.">[A-Za-z0-9_ ]+</validator>
    </xml>

    <token name="@PRESTO_URL_BASE@">https://presto.readthedocs.io/en/latest/tools</token>
    
    <!-- When modifying this file ensure that the version here matches the version above in requirements. -->
    <token name="@PRESTO_VERSION@">0.5.4</token>
    
    <token name="@HELP_NOTE@"><![CDATA[

====

**Note about limitations of pRESTO tools within Galaxy:**

pRESTO tools in galaxy have the following limitations vs. when run at the command line:

* Inputs must be FASTQ format and cannot be FASTA format.
* Multiple inputs files are not supported per argument (e.g. ``-1``, ``-2`` or ``-s``), i.e.
    - Steps that take a pair of fastq inputs can only take two files, not two sets of files
    - Steps that take a single set of fastq inputs can only take a single file
* The ``--outdir`` and ``--outname`` options are not supported; output files are named directly
    ]]></token>
</macros>