view basecoverage.xml @ 6:4d584cf5ced5 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit 200bd4645dd768eb6ee1aab7d181b76d34d13d4c

<tool id="gops_basecoverage_1" name="Base Coverage" version="1.0.0">
    <description>of all intervals</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <code file="operation_filter.py"/>
    <command><![CDATA[
python '$__tool_directory__/gops_basecoverage.py'
'$input1'
'$output'
-1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
    ]]></command>
    <inputs>
        <param name="input1" type="data" format="interval" label="Compute coverage for" />
    </inputs>
    <outputs>
        <data name="output" format="txt" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="1.bed" />
            <output name="output" file="gops_basecoverage_out.txt" />
        </test>
        <test>
            <param name="input1" value="gops_bigint.interval" />
            <output name="output" file="gops_basecoverage_out2.txt" />
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns.

This operation counts the total bases covered by a set of intervals.  Bases that are covered by more than one interval are **not** counted more than once towards the total.

@SCREENCASTS@

**Example**

.. image:: gops_baseCoverage.gif
    ]]></help>
</tool>