comparison multiBamSummary.xml @ 2:46909e251980 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11

1:92231fb0adda

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

        <conditional name="mode">
            <param name="modeOpt" type="select" label="Choose computation mode" 
                    help="In the bins mode, the coverage is computed for equally
                    sized bins. In the BED file mode, a list of genomic regions in BED
                    format has to be given. For each region in the BED file the number of
                    overlapping reads is counted in each of the BAM files.
                    ">
                <option value="bins" selected="true">Bins</option>
                <option value="BED-file">Limit calculation to certain regions (BED file)</option>
            </param>
            <when value="bins">

                <expand macro="distanceBetweenBins" />

            </when>
            <when value="BED-file">
                <param name="region_file" type="data" format="bed"
                    label="Region file in BED format"
                    help="Coverage is computed for the number of reads that overlap such regions."/>
            </when>
        </conditional>

        <expand macro="region_limit_operation" />

    </tests>
    <help>
<![CDATA[

**What it does**

This tool generates a matrix of read-coverages for a list of genomic regions and at least two samples (BAM files).
The genome is split into bins of the given size. For each bin, the number of reads found in it in each BAM file is counted.
Alternatively, a bed file with pre-defined genomic regions can be provided. In each case the calculation can further be limited to
a given genomic interval (e.g. a given chromosome). This option is mostly used for testing and efficiency.
A typical follow-up application is to check and visualize the similarity between replicates or published data sets (see: plotPCA and plotCorrelation).

**Output files**:

- **score matrix**: a compressed matrix where every row corresponds to a genomic region (or bin) and each column corresponds to a sample (BAM file)
- Optional : Uncompressed **score matrix**, in case you want to analyse the coverage scores yourself. (Select to "Save raw counts" from above)

=======

.. image:: $PATH_TO_IMAGES/QC_multiBamSummary_humanSamples.png
   :alt: Heatmap of RNA Polymerase II ChIP-seq


You can find more details on the multiBamSummary doc page: https://deeptools.readthedocs.org/en/master/content/tools/multiBamSummary.html

-----

@REFERENCES@
]]>

2:46909e251980

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

        <conditional name="mode">
            <param name="modeOpt" type="select" label="Choose computation mode"
                    help="In the bins mode, the coverage is computed for equally
                    sized bins. \nIn BED file mode, a list of genomic regions
                    in BED or INTERVAL format has to be given. For each region
                    in the BED file, the number of overlapping reads from each BAM file is counted.
                    ">
                <option value="bins" selected="true">Bins</option>
                <option value="BED-file">Limit calculation to certain regions (BED file)</option>
            </param>
            <when value="bins">

                <expand macro="distanceBetweenBins" />

            </when>
            <when value="BED-file">
                <param name="region_file" type="data" format="bed"
                    label="Region file in BED or INTERVAL format"
                    help="Coverage is computed for the number of reads that overlap such regions."/>
            </when>
        </conditional>

        <expand macro="region_limit_operation" />

    </tests>
    <help>
<![CDATA[

What it does
-------------

This tool generates a matrix of read coverages for a list of genomic regions and at least two samples (BAM files).
The genome is split into bins of the given size. For each bin, the number of reads found in each BAM file is counted.
Alternatively, an interval file with pre-defined genomic regions can be provided.

In principle, this tool does the same as ``multiBigwigSummary``, but for BAM files.

A typical follow-up application is to check and visualize the similarity and variability between replicates or published data sets (see: ``plotPCA`` and ``plotCorrelation``).

Output
--------

The default output is a **compressed file** that can only be used with ``plotPCA`` or ``plotCorrelation``.

To analyze the coverage scores yourself, you can get the **uncompressed score matrix** where every row corresponds to a genomic region (or bin) and each column corresponds to a sample (BAM file). (To obtain this output file, select "Save raw counts (coverages) to file" )

.. image:: $PATH_TO_IMAGES/multiBamSummary_output.png
   :width: 600
   :height: 443

-----

@REFERENCES@
]]>