--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/piranha.xml	Fri Jul 24 06:05:39 2015 -0400
@@ -0,0 +1,162 @@
+<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>