<?xml version="1.0"?>
<macros>
	<xml name="citations">
		<citations>
			<citation type="doi">10.1371/journal.pcbi.1004401</citation>
			<yield />
		</citations>
	</xml>
	<xml name="requirements">
		<requirements>
			<requirement type="package" version="@VERSION@">transit</requirement>
			<yield />
		</requirements>
	</xml>
	<token name="@VERSION@">2.3.1</token>
	<xml name="outputs">
        <yield />
        <data name="sites" from_work_dir="transit_out.txt" format="tabular" label="${tool.name} on ${on_string} Sites" />
    </xml>
    <xml name="replicates">
        <param name="replicates" type="select" label="How to handle replicates">
        	<option value="Mean">Mean</option>
        	<option value="Sum">Sum</option>
        </param>
    </xml>
    <xml name="inputs">
        <param name="inputs" type="data" format="wig,tabular" multiple="true" label="Input .wig files" />
        <yield />
        <param name="annotation" type="data" format="gff3" label="Input annotation" />
    </xml>
    <xml name="ignore_tas">
        <param name="nterm" argument="-iN" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the N terminus." />
        <param name="cterm" argument="-iC" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the C terminus." />
    </xml>
    <xml name="standard_inputs">
    	<expand macro="inputs" />
    	<yield />
    	<expand macro="ignore_tas" />
    </xml>
    <token name="@LINK_INPUTS@">
        <![CDATA[
            #set $input_files = ','.join(['input_file_%d.wig' % idx for idx, _ in enumerate(str($inputs).split(','))])
            #for idx, filename in enumerate(str($inputs).split(',')):
                ln -s '$filename' input_file_${idx}.wig &&
            #end for
            ln -s '$annotation' annotation.dat &&
        ]]>
    </token>
    <token name="@STANDARD_OPTIONS@">
        -iN $nterm
        -tC $cterm
    </token>
</macros>