<tool id="piranha" name="Piranha" version="0.1.0">
    <description>peak-caller for CLIP- and RIP-Seq data</description>
    <requirements>
        <requirement type="package" version="1.2.1">piranha</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        ln -s $input ./foo.$input.ext &&

        Piranha
        $sort
        #if $p_threshold:
            -p $p_threshold
        #end if
        $no_pval_correct
        #if $background_thresh:
            -a $background_thresh
        #end if
        #if $bin_size_reponse:
            -b $bin_size_reponse
        #end if
        #if $bin_size_covars:
            -i $bin_size_covars
        #end if
        #if $bin_size_both:
            -z $bin_size_both
        #end if
        #if $merge_bins.merge=="yes":
            -u $merge_bins.cluster_dist
        #else:
            -u $merge_bins.merge
        #end if
        $print_covars
        $fit
        #if $dist:
            -d $dist
        #end if
        $fitMethod
        #if $model:
            -m $model
        #end if
        $stranded
        $no_normalisation
        $log_covars
        ./foo.$input.ext
        #for $covariate in $covariates:
            $covariate.covariate_file
        #end for

        -o ./piranha.out
    ]]></command>
    <inputs>
        <param name="input" type="data" format="bed,bam" label="Choose input BED or BAM file"/>
        <repeat name="covariates" title="Choose covariate">
            <param name="covariate_file" type="data" format="bed" label="Choose covariate BED file"/>
        </repeat>
        <param name="sort" type="boolean" label="Is your input file already sorted?" checked="False" falsevalue="-s" truevalue=""/>
        <param name="p_threshold" type="float" min="0" max="1" value="1" label="Significance threshold for sites"/>
        <param name="no_pval_correct" type="boolean" checked="False" falsevalue="" truevalue="-c"
            label="Disable p-values correction for multiple hypothesis testing?" help="We correct by default using B &amp; H."/>
        <param name="background_thresh" type="float" optional="true"
            label="Indicates that this proportion of the lowest scores should be considered the background"/>
        <param name="bin_size_reponse" type="integer" optional="true"
            label="Indicates that input is raw reads and should be binned into bins of this size"/>
        <param name="bin_size_covars" type="integer" optional="true"
            label="Indicates that the covariates are raw reads and should be binned into bins of this size"/>
        <param name="bin_size_both" type="integer" optional="true" label="Synonymous with -b x -i x for any x"/>
        <conditional name="merge_bins">
            <param name="merge" type="select" label="Merge significant bins within certain distance?">
                <option value="yes">Yes</option>
                <option value="0" selected="true">No</option>
            </param>
            <when value="yes">
                <param name="cluster_dist" type="integer" value="1" label="Merge significant bins within this distance"
                help="Default is 1 (merge adjacent)"/>
            </when>
        </conditional>
        <param name="print_covars" type="boolean" checked="True" truevalue="" falsevalue="-r"  label="Print covariate values in output" help="(-r)" />
        <param name="fit" type="boolean" checked="False" truevalue="-f" falsevalue="" label="Fit only" />
        <param name="dist" type="select" label="Select distribution type">
            <option value="">None</option>
            <option value="Poisson">Poisson</option>
            <option value="NegativeBinomial">NegativeBinomial</option>
            <option value="ZeroTruncatedPoisson">ZeroTruncatedPoisson</option>
            <option value="ZeroTruncatedNegativeBinomial">ZeroTruncatedNegativeBinomial</option>
            <option value="PoissonRegression">PoissonRegression</option>
            <option value="NegativeBinomialRegression">NegativeBinomialRegression</option>
            <option value="ZeroTruncatedPoissonRegression">ZeroTruncatedPoissonRegression</option>
            <option value="ZeroTruncatedNegativeBinomialRegression">ZeroTruncatedNegativeBinomialRegression</option>
        </param>
        <param name="fitMethod" type="boolean" checked="False" truevalue="-t"
            falsevalue="" label="Use component fitting method"  help="(-t)"/>
        <param name="model" type="data" optional="True" format="xml" label="Select the model file"/>

        <param name="stranded" type="boolean" checked="True" truevalue=""
            falsevalue="-x" label="Preserve strand information"
            help="If not set all the peaks will be associated to the positive strand. (-x)"/>
        <param name="no_normalisation" type="boolean" checked="yes" falsevalue="-n" 
            truevalue="" label="Normalise covariates?" help="(-n)"/>
        <param name="log_covars" type="boolean" checked="False" truevalue="-l" 
            falsevalue="" label="Convert covariates to log scale?" help="(-l)"/>
    </inputs>
    <outputs>
        <data format="tabular" name="output_bed" from_work_dir="piranha.out"
            label="${tool.name} on ${on_string}: BED with p-values">
            <filter>fit is False</filter>
        </data>
        <data format="xml" name="output_xml" from_work_dir="piranha.out"
            label="${tool.name} on ${on_string}: Model file">
            <filter>fit is True</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="zntbr_unbinned_response.bed" ftype="bed"/>
            <repeat name="covariates">
                <param name="covariate_file" value="ztnbr_binning_cov1.bed" ftype="bed"/>
            </repeat>
            <repeat name="covariates">
                <param name="covariate_file" value="ztnbr_binning_cov2.bed" ftype="bed"/>
            </repeat>
            <param name="fit" value="True"/>
            <param name="bin_size_reponse" value="1"/>
            <param name="background_thresh" value="1"/>
            <output name="output_xml" file="ztnbrBinningTestModelOutput.expected.xml" ftype="xml"/>
        </test>
        <test>
            <param name="input" value="testPrianha_zntb_unbinned.bam" ftype="bam"/>
            <param name="fit" value="True"/>
            <param name="bin_size_reponse" value="1"/>
            <param name="background_thresh" value="1"/>
            <output name="output_xml" file="ztnbBinningTestModelOutput.expected.xml" ftype="xml"/>
        </test>
        <test>
            <param name="input" value="ztnbSimpleTest_response.bed" ftype="bed"/>
            <param name="no_pval_correct" value="True"/>
            <param name="p_threshold" value="1"/>
            <param name="background_thresh" value="1"/>
            <param name="-" value="ZeroTruncatedNegativeBinomial"/>
            <output name="output_xml" file="ztnbSimpleTest_output.expected.bed" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

`Piranha <http://smithlabresearch.org/software/piranha/>`_  is a peak-caller for CLIP- and RIP-Seq data. It takes input in BED or BAM format and identifies regions of statistically significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process. 


    ]]></help>
    <citations>
        <citation type="bibtex">
            @ARTICLE{bgruening_galaxytools,
                Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},
                keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna},
                title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},
                url = {https://github.com/bgruening/galaxytools}
            }
        </citation>
    </citations>
</tool>