# HG changeset patch # User jjohnson # Date 1613950853 0 # Node ID 0ad5327b80cc1ff86306a7d66370a365a9c1abbf "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722" diff -r 000000000000 -r 0ad5327b80cc fgbio_call_molecular_consensus_reads.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fgbio_call_molecular_consensus_reads.xml Sun Feb 21 23:40:53 2021 +0000 @@ -0,0 +1,107 @@ + + Calls consensus sequences from reads with the same unique molecular tag + + macros.xml + + + fgbio --version + + + + + +
+ + + + +
+ +
+ + + + + + + + + +
+ + +
+ + + output_rejects == True + + + + + +
diff -r 000000000000 -r 0ad5327b80cc macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Feb 21 23:40:53 2021 +0000 @@ -0,0 +1,56 @@ + + 1.3.0 + 0 + + + fgbio + + + + (([1-9][0-9]*[TBMS])*([+]|[1-9][0-9]*)[TBMS]) + @READ_STRUCTURE_PATTERN@(\s@READ_STRUCTURE_PATTERN@)* + + ^@READ_STRUCTURES_PATTERN@$ + + + ^[A-Za-z][A-Za-z]$ + + + + + + + + + + + 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 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 + + +]]> + + + + + +