<tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0">
    <description>assesses the sequencing depth of BAM/CRAM files </description>
    <macros>
        <token name="@BINARY@">plotCoverage</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command>
<![CDATA[
        #set files=[]
        #set labels=[]

        @multiple_input_bams@

        @BINARY@

            @THREADS@

            --plotFile '$outFileName'
            --bamfiles #echo " ".join($files)#
            --labels #echo " ".join($labels)#
            --plotFileFormat "$outFileFormat"

            #if $outRawCounts:
                --outRawCounts '$outFileRawCounts'
            #end if

            #if $advancedOpt.showAdvancedOpt == "yes":
                --numberOfSamples '$advancedOpt.numberOfSamples'
                $advancedOpt.skipZeros

                #if str($advancedOpt.region).strip() != '':
                    --region '$advancedOpt.region'
                #end if
                --numberOfSamples $advancedOpt.numberOfSamples

                #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
                    --plotTitle '$advancedOpt.plotTitle'
                #end if
                @ADVANCED_OPTS_READ_PROCESSING@
                @PLOTWIDTHHEIGHT@
                @blacklist@
            #end if

]]>
    </command>
    <inputs>

        <expand macro="multiple_input_bams" MIN="1"/>

        <conditional name="advancedOpt">
            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <param argument="--numberOfSamples" type="integer" value="100000" min="1"
                   label="Number of samples"
                   help="Number of samples taken from the genome to compute the scaling factors."/>
                <expand macro="plotWidthHeight" PLOTWIDTH="15.0" PLOTHEIGHT="5.0" />
                <expand macro="region_limit_operation" />
                <expand macro="read_processing_options" />
                <expand macro="skipZeros" />
                <expand macro="plotTitle" />
                <expand macro="blacklist" />
            </when>
        </conditional>

        <expand macro="input_image_file_format" />
        <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to a file" help=""/>


    </inputs>
    <outputs>
        <expand macro="output_image_file_format_not_nested" />
        <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
            <filter>outRawCounts is True</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
            <!--param name="outFileFormat" value="png" /-->
            <param name="showAdvancedOpt" value="yes" />
            <param name="plotTitle" value="Test Title from Galaxy" />
            <param name="outRawCounts" value="True" />
            <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" />
            <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" />
        </test>
    </tests>
    <help>
<![CDATA[
What it does
-------------

This tool is useful to **assess the sequencing depth** of a given sample.
It samples 1 million bp, counts the number of overlapping reads and reports
a coverage histogram that tells you how many bases are covered how many times.

**Note:** Multiple BAM files are accepted but all should correspond to the same genome assembly.

Output
---------

The default output is a **panel of two plots** (see below for an example): One is a density plot visualizing the frequencies of read coverages, the other one lets you estimate what fraction of the genome has a depth of sequencing of, for example, 2 overlapping reads or more.

The optional output is a table where each row represents the number of reads overlapping with a sampled bp.

.. image:: $PATH_TO_IMAGES/plotCoverage_output.png
   :width: 600
   :height: 345

Example plot
-----------------

.. image:: $PATH_TO_IMAGES/plotCoverage_annotated.png
   :width: 600
   :height: 291


@REFERENCES@
]]>
    </help>
    <expand macro="citations" />
</tool>