comparison plotCoverage.xml @ 1:edc6597ff21e draft

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

0:268ab1ca4091

<tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0">
    <description>plots a histogram of coverage on genomic regions </description>
    <macros>
        <token name="@BINARY@">plotCoverage</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <expand macro="requirements"/>

            <!--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="100" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

This tools samples 1 million positions in the genome to build
a coverage histogram. Multiple bam files are accepted but all should
correspond to the same genome assembly.


@REFERENCES@
]]>
    </help>

1:edc6597ff21e

<tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0">
    <description>assesses the sequencing depth of BAM files </description>
    <macros>
        <token name="@BINARY@">plotCoverage</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <expand macro="requirements"/>

            <!--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="500" />
        </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>