view basecoverage.xml @ 4:2cedec3759e4 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689

<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>