view macros.xml @ 0:fb20fa735dfe draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/vcfanno/ commit d962b44c5d3fecd1a315d6fbda8831d6de1b2801"

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">0.3.2</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">20.01</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">vcfanno</requirement>
            <requirement type="package">tabix</requirement>
            <requirement type="package">samtools</requirement>
        </requirements>
    </xml>
    <xml name="version_command">
        <version_command>vcfanno --help</version_command>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">@online{vcfanno,
              author = {Brent S. Pedersen},
              title = {vcfanno},
              year = 2016,
              url = {https://github.com/brentp/vcfanno},
              urldate = {2020-12-03}
            }</citation>
            <citation type="doi">10.1186/s13059-016-0973-5</citation>
        </citations>
    </xml>
    <xml name="xrefs">
        <xrefs>
            <xref type="bio.tools">vcfanno</xref>
        </xrefs>
    </xml>

    <!--
        Inputs
    -->
    <macro name = "ops">
        <option value="self" selected="true">self - pull directly from the annotation and handle multi-allelics</option>
        <option value="concat">concat - comma delimited list of output</option>
        <option value="count">count - count the number of overlaps</option>
        <option value="div2">div2 - given two values a and b, return a / b</option>
        <option value="first">first - take only the first value</option>
        <option value="flag">flag - presense/absence via VCF flag</option>
        <option value="max">max (numbers only)</option>
        <option value="mean">mean (numbers only)</option>
        <option value="min">min (numbers only)</option>
        <option value="sum">sum (numbers only)</option>
        <option value="uniq">uniq - comma-delimited list of uniq values</option>
        <option value="by_alt">by_alt - comma-delimited by alt (Number=A), pipe-delimited (|) for multiple annos for the same alt.</option>
        <yield/>
    </macro>

    <!--
        Help
    -->

    <token name="@WID@"><![CDATA[
*vcfanno* allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files. It uses a simple conf file to allow the user to specify the source annotation files and fields and how they will be added to the info of the query VCF.

 - For VCF, values are pulled by name from the INFO field with special-cases of ID and FILTER to pull from those VCF columns.
 
 - For BED, values are pulled from (1-based) column number.
 
 - For BAM, depth (count), "mapq" and "seq" are currently supported.
 ]]></token>
    <token name="@REFERENCES@"><![CDATA[
More information are available in the `mailing list <https://groups.google.com/g/vcfanno>`_ and `github <https://github.com/brentp/vcfanno>`_.
    ]]></token>
</macros>