Mercurial > repos > jjohnson > fgbio_group_reads_by_umi
diff macros.xml @ 1:568816308859 draft
"planemo upload commit 692ea558cbbefee93859dc2b005fab5ac4970eb8"
| author | jjohnson |
|---|---|
| date | Wed, 24 Feb 2021 13:02:09 +0000 |
| parents | 900cd2865768 |
| children | 9efbd847e5d1 |
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--- a/macros.xml Sun Feb 21 23:40:34 2021 +0000 +++ b/macros.xml Wed Feb 24 13:02:09 2021 +0000 @@ -17,22 +17,33 @@ </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 + - 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: