view basecoverage.xml @ 5:21898544368b draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit d7b1a60c0aecc46b7f625c3e32f882562b512fd9

<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>