annotate macros.xml @ 3:fa7c3a74acf2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 16a919905f336e34e237388c1921d0f4f8a368af

<macros>
    <token name="@TOOL_VERSION@">4.11</token>
    <!-- HOMER index version compatible with this version of HOMER
    This is the HOMER version that introduced the preparsed structure expected
    by the current version. -->
    <token name="@IDX_VERSION@">4.11</token>
    <token name="@VERSION_SUFFIX@">3</token>
    <token name="@PROFILE@">20.05</token>
    <xml name="xrefs">
        <xrefs>
            <xref type="bio.tools">homer</xref>
        </xrefs>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">homer</requirement>
        </requirements>
    </xml>
    <xml name="choose_center">
        <conditional name="choose_center">
            <param name="center" type="select" label="Do you want to center your sequence on the peak center?">
                <option value="centered" selected="True">Yes</option>
                <option value="manual">No, I want asymetric (raise an error if given was chosen above)</option>
            </param>
            <when value="centered"/>
            <when value="manual">
                <param name="sizes" type="integer" value="-100" label="sequence start relative to center"/>
            </when>
        </conditional>
    </xml>
    <xml name="mask_size">
        <param argument="-mask" type="boolean" truevalue="True" falsevalue="False" label="mask repeats/lower case sequence"/>
        <conditional name="fixed_size">
            <param name="size_fixed" type="select" label="Do you want a fixed fragment size?">
                <option value="fixed" selected="True">Yes</option>
                <option value="given">No, I want to keep the size of my peaks (-size given)</option>
            </param>
            <when value="given"/>
            <when value="fixed">
                <param argument="-size" type="integer" min="0" value="200" label="fragment size in bp"/>
                <expand macro="choose_center"/>
            </when>
        </conditional>
    </xml>
    <xml name="geneid_input">
        <param name="organism" type="select" label="What is the organism DB to be used?">
            <options from_data_table="homer_promoters">
                <filter type="sort_by" column="organism"/>
                <validator type="no_options" message="No pre-installed organism DBs are available. Contact your galaxy administrator."/>
            </options>
        </param>
        <param name="target_set" type="data" format="tabular" label="List of gene identifiers for the positive set"/>
    </xml>
    <xml name="citation">
        <citations>
            <citation type="doi">10.1016/j.molcel.2010.05.004</citation>
        </citations>
    </xml>
</macros>