<?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>
            <requirement type="package" version="3.7">python</requirement>
			<yield />
		</requirements>
	</xml>
	<token name="@VERSION@">3.0.1</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="handle_replicates">
        <param name="handle_replicates" type="select" label="How to handle replicates" value="Mean">
        	<option value="Sum">Sum</option>
        	<option value="Mean">Mean</option>
        </param>
    </xml>
    <xml name="inputs">
        <conditional name="mode">
            <param name="replicates" type="select" label="Operation mode" help="If set to 'Batch', transit will run and produce one output for each input file. If set to 'Replicates', transit will run once on all the input files.">
                <option value="Batch">Batch</option>
                <option value="Replicates">Replicates</option>
            </param>
            <when value="Batch">
                <param name="inputs" type="data" format="wig,tabular" multiple="false" label="Input .wig files" />
            </when>
            <when value="Replicates">
                <param name="inputs" type="data" format="wig,tabular" multiple="true" label="Input .wig files" />
            </when>
        </conditional>
        <yield />
        <param name="annotation" type="data" format="gff3,tabular" 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="normal">
        <param name="normalization" argument="-n" type="select" label="Normalization method"  value="TTR">
            <option value="TTR">TTR</option>
            <option value="nonorm">No Normalization</option>
            <option value="nzmean">Non-Zero Mean</option>
            <option value="totreads">Total read counts</option>
            <option value="zinfnb">Zero inflated Negative Binomial model</option>
            <option value="quantile">Quantile Normalization</option>
            <option value="betageom">Beta-Geometric Correction</option>
        </param>
    </xml>
    <xml name="standard_inputs">
    	<expand macro="inputs" />
    	<yield />
    	<expand macro="ignore_tas" />
    	<expand macro="normal" />
    </xml>
    <token name="@LINK_INPUTS@">
        <![CDATA[
            #if str($mode.replicates) == 'Batch':
                #set $input_files = $mode.inputs
            #else:
                #set $input_files = ','.join(['input_file_%d.wig' % idx for idx, _ in enumerate(str($mode.inputs).split(','))])
                #for idx, filename in enumerate(str($mode.inputs).split(',')):
                    ln -s '$filename' input_file_${idx}.wig &&
                #end for
            #end if
            ln -s '$annotation' annotation.dat &&
        ]]>
    </token>
    <token name="@STANDARD_OPTIONS@">
        -iN $nterm
        -tC $cterm
        -n $normalization
        -r $handle_replicates
    </token>
</macros>