<?xml version="1.0"?>
<tool id="idr" name="IDR" version="@VERSION@">
    <description>compare ranked list of identifications</description>
    <macros>
        <token name="@VERSION@">2.0.3</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">idr</requirement>
    </requirements>
    <command detect_errors="aggressive">
        <![CDATA[
        idr --samples '$primus' '$secundus'
        #if $peak_list:
            --peak-list '$peak_list'
        #end if
        #if $input_file_type:
            #if $primus.dataset.ext == 'gff':
                --input-file-type gff
            #else:
                --input-file-type $input_file_type
            #end if
        #end if
        #if $idr_threshold:
            --idr-threshold $idr_threshold
        #end if
        #if $rank != 'default':
            --rank $rank
        #end if
        --output-file idrValues.bed
        --soft-idr-threshold $soft_idr_threshold
        $plot $use_nonoverlapping_peaks --peak-merge-method $peak_merge_method
        --initial-mu $initial_mu --initial-sigma $initial_sigma --initial-rho $initial_rho
        --initial-mix-param $initial_mix_param $fix_mu $fix_sigma
        $dont_filter_peaks_below_noise_mean $use_best_multisummit_idr
        $allow_negative_scores --random-seed $random_seed --max-iter $max_iter
        --convergence-eps $convergence_eps $only_merge_peaks
        ]]>
    </command>
    <inputs>
        <param name="primus" argument="--samples" type="data" format="bed,gff" label="First set of peaks in GFF or BED format" />
        <param name="secundus" argument="--samples" type="data" format="bed,gff" label="Second set of peaks in GFF or BED format" />
        <param name="peak_list" argument="--peak-list" type="data" format="bed,gff" optional="True" label="List of peaks to filter by" />
        <param name="input_file_type" argument="--input-file-type" type="select" label="Input BED format" help="This option is ignored if the input file is GFF">
            <option value="" selected="true">Vanilla BED</option>
            <option value="gff">GFF</option>
            <option value="broadPeak">ENCODE broadPeak</option>
            <option value="narrowPeak">ENCODE narrowPeak</option>
        </param>
        <param argument="--rank" type="select" label="Column to use for ranking peaks">
            <option value="default">Use default</option>
            <option value="signal.value">signal</option>
            <option value="p.value">p value</option>
            <option value="q.value">q value</option>
        </param>
        <param name="idr_threshold" argument="--idr-threshold" type="float" optional="true" value="" />
        <param name="soft_idr_threshold" argument="--soft-idr-threshold" type="float" value="0.05" />
        <param argument="--plot" type="boolean" truevalue="--plot" falsevalue="" label="Output PNG plot of peaks" />
        <param name="use_nonoverlapping_peaks" argument="--use-nonoverlapping-peaks" type="boolean" truevalue="--use-nonoverlapping-peaks" falsevalue="" label="Use peaks without an overlapping match and set the value to 0" />
        <param name="peak_merge_method" argument="--peak-merge-method" type="select" label="Method to use for merging peaks">
            <option value="sum">Sum</option>
            <option value="avg">Average</option>
            <option value="min">Min</option>
            <option value="max">Max</option>
        </param>
        <param name="initial_mu" argument="--initial-mu" type="float" value="0.1" label="Initial value of mu" />
        <param name="initial_sigma" argument="--initial-sigma" type="float" value="1.0" label="Initial value of sigma" />
        <param name="initial_rho" argument="--initial-rho" type="float" value="0.2" label="Initial value of rho" />
        <param name="initial_mix_param" argument="--initial-mix-param" type="float" value="0.5" label="Initial value of the mixture parameters" />
        <param name="fix_mu" argument="--fix-mu" type="boolean" truevalue="--fix-mu" falsevalue="" label="Fix mu to the starting point and do not let it vary" />
        <param name="fix_sigma" argument="--fix-sigma" type="boolean" truevalue="--fix-sigma" falsevalue="" label="Fix sigma to the starting point and do not let it vary" />
        <param name="dont_filter_peaks_below_noise_mean" argument="--dont-filter-peaks-below-noise-mean" type="boolean" truevalue="--dont-filter-peaks-below-noise-mean" falsevalue="" label="Allow signal points that are below the noise mean" />
        <param name="use_best_multisummit_idr" argument="--use-best-multisummit-IDR" type="boolean" truevalue="--use-best-multisummit-IDR" falsevalue="" label="Set the IDR value for a group of multi summit peaks" help="A group of peaks with the same chr/start/stop but different summits" />
        <param name="allow_negative_scores" argument="--allow-negative-scores" type="boolean" truevalue="--allow-negative-scores" falsevalue="" label="Allow negative values for scores" />
        <param name="random_seed" argument="--random-seed" type="integer" value="0" label="The random seed value" />
        <param name="max_iter" argument="--max-iter" type="integer" value="3000" label="The maximum number of optimization iterations" />
        <param name="convergence_eps" argument="--convergence-eps" type="float" value="0.000001" label="The maximum change in parameter value changes for convergence" />
        <param name="only_merge_peaks" argument="--only-merge-peaks" type="boolean" truevalue="--only-merge-peaks" falsevalue="" label="Only return the merged peak list" />
    </inputs>
    <outputs>
        <data format="bed" name="idr_values" from_work_dir="idrValues.bed" label="${tool.name} on ${on_string}: IDR Values">
            <actions>
                <action type="format">
                    <option type="from_param" name="primus" param_attribute="ext" />
                </action>
            </actions>
        </data>
        <data format="png" name="idr_plot" from_work_dir="idrValues.bed.png" label="${tool.name} on ${on_string}: PNG Plot">
            <filter>plot</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="primus" value="idr_input1.1.bed" ftype="bed" />
            <param name="secundus" value="idr_input1.2.bed" ftype="bed" />
            <param name="rank" value="default" />
            <param name="plot" value="True" />
            <output name="idr_values" file="idr_out1.bed" ftype="bed" />
            <output name="idr_plot" file="idr_out1.png" ftype="png" compare="sim_size" delta="1000"/>
        </test>
        <test>
            <param name="primus" value="idr_input2.1.bed" ftype="bed" />
            <param name="secundus" value="idr_input2.2.bed" ftype="bed" />
            <param name="rank" value="default" />
            <param name="plot" value="True" />
            <output name="idr_values" file="idr_out2.bed" ftype="bed" />
            <output name="idr_plot" file="idr_out2.png" ftype="png" compare="sim_size" delta="1000"/>
        </test>
        <test>
            <param name="primus" value="idr_input3.1.bed" ftype="bed" />
            <param name="secundus" value="idr_input3.2.bed" ftype="bed" />
            <param name="peak_list" value="idr_input3.3.bed" ftype="bed" />
            <param name="rank" value="default" />
            <param name="plot" value="True" />
            <output name="idr_values" file="idr_out3.bed" ftype="bed" />
            <output name="idr_plot" file="idr_out3.png" ftype="png" compare="sim_size" delta="1000"/>
        </test>
        <test>
            <param name="primus" value="idr_input4.1.gff" ftype="gff" />
            <param name="secundus" value="idr_input4.2.gff" ftype="gff" />
            <param name="input_file_type" value="gff" />
            <param name="rank" value="default" />
            <param name="plot" value="True" />
            <output name="idr_values" file="idr_out4.gff" ftype="gff" />
            <output name="idr_plot" file="idr_out4.png" ftype="png" compare="sim_size" delta="1000"/>
        </test>
     </tests>
    <help>
<![CDATA[
The `IDR <https://github.com/nboley/idr/blob/master/README.md>`__ (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility. Unlike the usual scalar measures of reproducibility, the IDR approach creates a curve, which quantitatively assesses when the findings are no longer consistent across replicates.
]]>
    </help>
    <citations>
        <citation type="doi">10.1214/11-AOAS466</citation>
    </citations>
</tool>