annotate bamFingerprint.xml @ 31:7889d260cc37 draft default tip

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty

<tool id="deeptools_bamFingerprint" name="bamFingerprint" version="@WRAPPER_VERSION@.0">
    <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description>
    <macros>
        <token name="@BINARY@">bamFingerprint</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
<![CDATA[
        @multiple_input_bams@

        bamFingerprint

            @THREADS@

            --bamfiles #echo " ".join($files)
            --labels #echo " ".join($labels)

            --fragmentLength $fragmentLength

            --plotFile $outFileName

            #if $output.showOutputSettings == "yes"
                --plotFileFormat $output.outFileFormat
                #if $output.saveRawCounts:
                    --outRawCounts '$outFileRawCounts' 
                #end if
            #else
                --plotFileFormat 'png'
            #end if

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

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

                $advancedOpt.doNotExtendPairedEnds
                $advancedOpt.ignoreDuplicates
                $advancedOpt.skipZeros

                #if $advancedOpt.minMappingQuality:
                --minMappingQuality '$advancedOpt.minMappingQuality'
                #end if

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

            #end if
]]>
    </command>

    <inputs>
        <expand macro="multiple_input_bams" />
        <expand macro="fragmentLength" />
        <expand macro="region_limit_operation" />

        <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 name="binSize" type="integer" value="500" min="1" 
                   label="Bin size in bp"
                   help="Length in base pairs for a window used to sample the genome."/>
                <param name="numberOfSamples" type="integer" value="100000" min="1" 
                   label="Number of samples"
                   help="Number of samples taken from the genome to compute the scaling factors. (--numberOfSamples)"/>
                <expand macro="doNotExtendPairedEnds" />
                <expand macro="ignoreDuplicates" />
                <expand macro="minMappingQuality" />
                <expand macro="skipZeros" />
                <expand macro="plotTitle" />
            </when>
        </conditional>
        <conditional name="output">
            <param name="showOutputSettings" type="select" label="Show advanced output settings">
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <expand macro="input_image_file_format" />
                <param name="saveRawCounts" type="boolean" label="Save the bin counts" help="(--outRawCounts)"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <expand macro="output_image_file_format" />
        <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
            <filter>
            ((
                output['showOutputSettings'] == 'yes' and 
                output['saveRawCounts'] is True
            ))
            </filter>
        </data>
    </outputs>
    <tests>
        <test>
            <repeat name="input_files">
                <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" />
            </repeat>
            <repeat name="input_files">
                <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" />
            </repeat>
            <param name="fragmentLength" value="200" />
            <param name="showAdvancedOpt" value="no" />
            <param name="showOutputSettings" value="no" />
            <output name="outFileName" file="bamFingerprint_result1.png" ftype="png" compare="sim_size" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

This tool is useful to assess the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background signal)
and it is based on a method developed by Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3).

The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of specified length.
These counts are then sorted according to their rank (the bin with the highest number of reads has the highest rank)
and the cumulative sum of read counts are plotted. An ideal input (control sample) with perfect uniform distribution of reads
along the genome (i.e. without enrichments in open chromatin etc.) should
generate a straight diagonal line. A very specific and strong ChIP enrichment will be indicated by a prominent and steep
rise of the cumulative sum towards the highest rank. This means that a big chunk of reads from the ChIP sample is located in
few bins which corresponds to high, narrow enrichments seen for transcription factors.


.. image:: $PATH_TO_IMAGES/QC_fingerprint.png


You can find more details on the bamFingerprint wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamFingerprint


**Output files**:

- Diagnostic plot
- Data matrix of raw counts

-----

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