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<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>
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