annotate plotCoverage.xml @ 28:9368fbc49c8b draft

planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9

<tool id="deeptools_plot_coverage" name="plotCoverage" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
    <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 ' '.join(map(str, $BED)) != 'None':
                #set bedFileList=[]
                #for $f in $BED:
                    #silent $bedFileList.append("'%s'" % $f)
                #end for
                #if $bedFileList != ["'None'"]:
                    --BED #echo ' '.join($bedFileList)#
                #end if
            #end if

            #if $coverageOpt.showCoverageOpt == "yes":
                --outCoverageMetrics '$outFileCoverageMetrics'
                #for $t in $coverageOpt.thresholds:
                    -ct $t.coverageThreshold
                #end for
            #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"/>
        <expand macro="custom_sample_labels" />
        <param argument="--BED" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
            label="Regions of interest"
            help="Limits the coverage analysis to the regions specified in these files. This overrides --numberOfSamples. It is inadvisable to combine this with saving the raw counts." />

        <conditional name="coverageOpt">
            <param name="showCoverageOpt" type="select" label="Show coverage metrics options">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <param argument="--outCoverageMetrics" type="boolean" label="Save per-threshold coverage metrics?"/>
                <repeat name="thresholds" title="Coverage Thresholds">
                    <param argument="--coverageThreshold" type="integer" min="0" label="Coverage Threshold" value="0"/>
                </repeat>
            </when>
        </conditional>

        <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 ${on_string}: bin counts">
            <filter>outRawCounts is True</filter>
        </data>
        <data format="tabular" name="outFileCoverageMetrics" label="${tool.name} on ${on_string}: Threshold Metrics">
            <filter>coverageOpt.outCoverageMetrics 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>
        <test>
            <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
            <param name="showAdvancedOpt" value="yes" />
            <param name="plotTitle" value="Test Title from Galaxy" />
            <param name="showCoverageOpt" value="yes" />
            <param name="coverageThreshold" value="0" />
            <param name="coverageThreshold" value="5" />
            <param name="coverageThreshold" value="10" />
            <param name="coverageThreshold" value="20" />
            <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" />
            <output name="outFileCoverageMetrics" file="plotCoverage.metrics" ftype="tabular" />
        </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>