view crossmap_wig.xml @ 0:0e6f675cea09 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447

<tool id="crossmap_wig" name="CrossMap Wig" 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 wig
            '${chain_source.input_chain}'
            '${input_file}'
            '${output}'

            && mv '${output}.bw' '${output}'
            && mv '${output}.sorted.bgr' '${output2}'
    ]]></command>

    <inputs>
        <conditional name="seq_source">
            <expand macro="source" />
            <when value="cached">
                <param format="wig" name="input" type="data" label="Wiggle 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 format="wig" name="input" type="data" label="Wiggle file"/>
            </when>
        </conditional>
        <expand macro="chain" />
    </inputs>

    <outputs>
        <data format="wig" name="output" label="${tool.name} on ${on_string}" />
        <data format="wig" name="output2" label="${tool.name} (bedgraph) on ${on_string}" />
    </outputs>

    <tests>
    <!-- WIG - Doesn't understand fixedStep -->
        <test>
            <param name="index_source" value="history"/>
            <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/>
            <param name="input_chain" value="aToB.over.chain" ftype="csv"/>

            <output name="output" file="test_wig_01_output_a.bw"/>
            <output name="output2" file="test_wig_01_output_a.sorted.bgr"/>
        </test>
    </tests>
    <help><![CDATA[
@HELP_GENERAL@

Wig
---

    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>