comparison multiBigwigSummary.xml @ 1:3da3c3750962 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920

0:bb542efec3b7

<tool id="deeptools_multi_bigwig_summary" name="multiBigwigSummary" version="@WRAPPER_VERSION@.0">
    <description>calculates average read coverages for a list of two or more bigwig files</description>
    <macros>
        <token name="@BINARY@">multiBigwigSummary</token>
        <import>deepTools_macros.xml</import>
    </macros>
   <expand macro="requirements" />

                    help="Correlation is computed for the number of reads that overlap such regions."/>
            </when>
        </conditional>

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

    </inputs>
    <outputs>
        <data format="deeptools_coverage_matrix" name="outFile" label="${tool.name} on ${on_string}: correlation matrix" />
        <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">

            <output name="outFileName" file="multiBigwigSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
        </test-->
    </tests>
    <help>
<![CDATA[
**What it does**

Given two or more bigWig files, multiBigwigSummary computes the average scores for each of the files in every genomic region.
This analysis is performed for the entire genome by running the program in 'bins' mode, or for certain user selected regions
in 'BED-file' mode. Typically the output of multiBigwigSummary is used by other tools, such as 'plotCorrelation' or 'plotPCA',
for visualization and diagnostic purposes.


**Output files**:

- **Coverage scores**: Coverage scores computed and saved in a format appropriate for 'plotCorrelation' or 'plotPCA'.

- Data matrix (optional,select to save raw counts to a file above): If you want to have a look at the coverage values
  or compute statistics yourself using a different program (like R).

-----

@REFERENCES@
]]>

1:3da3c3750962

<tool id="deeptools_multi_bigwig_summary" name="multiBigwigSummary" version="@WRAPPER_VERSION@.0">
    <description>calculates average scores for a list of two or more bigwig files</description>
    <macros>
        <token name="@BINARY@">multiBigwigSummary</token>
        <import>deepTools_macros.xml</import>
    </macros>
   <expand macro="requirements" />

                    help="Correlation is computed for the number of reads that overlap such regions."/>
            </when>
        </conditional>

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

    </inputs>
    <outputs>
        <data format="deeptools_coverage_matrix" name="outFile" label="${tool.name} on ${on_string}: correlation matrix" />
        <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">

            <output name="outFileName" file="multiBigwigSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
        </test-->
    </tests>
    <help>
<![CDATA[

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

This tool computes the average scores for every genomic region for every bigWig file that is provided. In principle, it does the same as ``multiBamSummary``, but for bigWig files.

The analysis is performed for the entire genome by running the program in 'bins' mode, or for certain user selected regions (e.g., genes) in 'BED-file' mode.

Typically the output of ``multiBigwigSummary`` is used by other tools, such as ``plotCorrelation`` or ``plotPCA``, for visualization and diagnostic purposes.


Output
--------

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

To analyze the average 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/multiBigwigSummary_output.png
   :width: 600
   :height: 358

-----

@REFERENCES@
]]>