Mercurial > repos > jjohnson > fgbio_group_reads_by_umi
view macros.xml @ 1:568816308859 draft
"planemo upload commit 692ea558cbbefee93859dc2b005fab5ac4970eb8"
author | jjohnson |
---|---|
date | Wed, 24 Feb 2021 13:02:09 +0000 |
parents | 900cd2865768 |
children | 9efbd847e5d1 |
line wrap: on
line source
<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>