annotate macros.xml @ 1:cb58d1961fd3 draft

"planemo upload commit 692ea558cbbefee93859dc2b005fab5ac4970eb8"

<macros>
    <token name="@TOOL_VERSION@">1.3.0</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">fgbio</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@READ_STRUCTURE_PATTERN@">(([1-9][0-9]*[TBMS])*([+]|[1-9][0-9]*)[TBMS])</token>
    <token name="@READ_STRUCTURES_PATTERN@">@READ_STRUCTURE_PATTERN@(\s@READ_STRUCTURE_PATTERN@)*</token>
    <xml name="read_structures_validator">
            <validator type="regex" message="">^@READ_STRUCTURES_PATTERN@$</validator>
    </xml>
    <xml name="sam_tag_validator">
            <validator type="regex" message="">^[A-Za-z][A-Za-z]$</validator>
    </xml>
    <xml name="sam_sort_order">
        <param argument="--sort-order" type="select" optional="true" label="Sort BAM by">
            <option value="TemplateCoordinate">TemplateCoordinate</option>
            <option value="Coordinate">Coordinate</option>
            <option value="Queryname">Queryname</option>
            <option value="Random">Random</option>
            <option value="RandomQuery">RandomQuery</option>
        </param>
    </xml>
    
    <xml name="sort_order_change_format">
        <change_format>
            <when input="sort_order" value="Coordinate" format="bam" />
            <when input="sort_order" value="TemplateCoordinate" format="bam" />
            <when input="sort_order" value="QueryName" format="unsorted.bam" />
            <when input="sort_order" value="Random" format="unsorted.bam" />
            <when input="sort_order" value="RandomQuery" format="unsorted.bam" />
        </change_format>
    </xml>

    <token name="@READ_STRUCTURES_HELP@"><![CDATA[
**Read Structures**

Read structures are made up of <number><operator> pairs much like the CIGAR string in BAM files. Four kinds of operators are recognized:

 -  T identifies a template read
 -  B identifies a sample barcode read
 -  M identifies a unique molecular index read
 -  S identifies a set of bases that should be skipped or ignored

The last <number><operator> pair may be specified using a + sign instead of number to denote “all remaining bases”. This is useful if, e.g., fastqs have been trimmed and contain reads of varying length. For example to convert a paired-end run with an index read and where the first 5 bases of R1 are a UMI and the second five bases are monotemplate you might specify:

:: 

    --input r1.fq r2.fq i1.fq --read-structures 5M5S+T +T +B

Alternative if you know your reads are of fixed length you could specify:

:: 

    --input r1.fq r2.fq i1.fq --read-structures 5M5S65T 75T 8B


]]></token>
    <xml name="citations">
        <citations>
            <yield />
        </citations>
    </xml>
</macros>