# HG changeset patch # User iuc # Date 1713271867 0 # Node ID b0a1f128fa15d29a1022fb330e880bd9d81d7c77 # Parent 26ed6ceeeec15e203c5530c9e0e7154f113c7e74 planemo upload for repository https://github.com/open2c/pairtools commit edb9fd7a6734203070b623876e76ce4a0a164ed9 diff -r 26ed6ceeeec1 -r b0a1f128fa15 parse.xml --- a/parse.xml Tue Apr 09 10:12:50 2024 +0000 +++ b/parse.xml Tue Apr 16 12:51:07 2024 +0000 @@ -1,4 +1,4 @@ - + Find ligation pairs in alignments and create pairs. macros.xml @@ -8,7 +8,9 @@ pairtools parse '$sam_path' -c '$chroms_path' - $assembly + #if str($assembly_name).strip(): + --assembly '$assembly_name' + #end if -o '$output_parsed_pairs' --min-mapq '$min_mapq' --max-molecule-size '$max_molecule_size' @@ -27,7 +29,7 @@ - + @@ -112,6 +114,16 @@ + + + + + + + + + +