<?xml version='1.0' encoding='UTF-8'?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="3.14.0">bioconductor-edger</requirement>
            <requirement type="package" version="4.11.1">meme</requirement>
            <requirement type="package" version="0.5">multigps</requirement>
        </requirements>
    </xml>
    <xml name="stdio">
        <stdio>
            <exit_code range="1:"/>
            <exit_code range=":-1"/>
            <regex match="Error:"/>
            <regex match="Exception:"/>
        </stdio>
    </xml>
    <xml name="rd_cond">
        <conditional name="read_distribution_cond">
            <param name="read_distribution" type="select" label="Use read distribution file for this replicate?" help="Selecting No uses default distribution.">
                <option value="no" selected="True">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="yes">
                <param name="read_distribution_file" type="data" format="tabular" label="Read distribution file" />
            </when>
            <when value="no" />
        </conditional>
    </xml>
    <xml name="frc_param">
        <param  name="fixed_read_count" type="select" label="Use fixed per-base read count limit for this replicate?" help="Selecting No uses a global per-base limit that is estimated from a Poisson distribution.">
            <option value="no" selected="True">No</option>
            <option value="yes">Yes</option>
        </param>
    </xml>
    <xml name="motif_finding_params">
        <param name="memenmotifs" type="integer" min="0" value="3" label="Number of motifs MEME should find for each condition" />
        <param name="mememinw" type="integer" min="0" value="6" label="Minimum motif width for MEME" />
        <param name="mememaxw" type="integer" min="0" value="16" label="Maximum motif width for MEME" />
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1371/journal.pcbi.1003501</citation>
        </citations>
    </xml>
</macros>