comparison crossmap_bigwig.xml @ 0:fb5401ff7ca2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa

0:fb5401ff7ca2

<tool id="crossmap_bw" name="CrossMap BigWig" version="@WRAPPER_VERSION@-0">
    <description>Convert genome coordinates or annotation files between genome assemblies</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>

    <command><![CDATA[
        #set $input_file = str($seq_source.input)

        CrossMap.py bigwig
            '${chain_source.input_chain}'
            '${input_file}'
            '${output}'

            && mv '${output}.bw' '${output}'

    ]]></command>

    <inputs>
        <conditional name="seq_source">
            <expand macro="source" />
            <when value="cached">
                <param format="bigwig" name="input" type="data" label="BigWig file">
                    <validator type="unspecified_build"/>
                    <!-- Gives error in tests
                    <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build."/>
                    -->
                </param>
            </when>
            <when value="history">
                <param type="data" format="bigwig" name="input"       label="BigWig file"/>
            </when>
        </conditional>
        <expand macro="chain" />
    </inputs>

    <outputs>
        <data format="bigwig" name="output" label="${tool.name} on ${on_string}" />
    </outputs>

    <tests>
    <!-- BigWig --><!-- Malfuncioning in CrossMap 0.2, but patched via galaxy toolshed installer -->
        <test>
            <param name="input_format" value="bigwig"/>
            <param name="index_source" value="history"/>
            <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/>
            <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
            <param name="include_fails" value="False"/>

            <output name="output" file="test_bigwig_01_output_a.bw"/>
        </test>
    </tests>
    <help><![CDATA[
@HELP_GENERAL@

BigWig
------

    Input wiggle data can be in variableStep (for data with irregular
    intervals) or fixedStep (for data with regular intervals). Regardless of
    the input, the output will always in bedGraph format. bedGraph format is
    similar to wiggle format and can be converted into BigWig format using UCSC
    wigToBigWig tool. We export files in bedGraph because it is usually much
    smaller than file in wiggle format, and more importantly, CrossMap
    internally transforms wiggle into bedGraph to increase running speed.

Please see `the manual <http://crossmap.sourceforge.net/#convert-wiggle-bigwig-format-files>`__ for more details
]]></help>

    <citations>
        <citation type="doi">10.1093/bioinformatics/btt730</citation>
    </citations>
</tool>