# HG changeset patch # User stheil # Date 1443110321 14400 # Node ID 149ae07524e4c13c32adb3e58fb6f2d3b61a0943 Uploaded diff -r 000000000000 -r 149ae07524e4 idba_ud.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/idba_ud.xml Thu Sep 24 11:58:41 2015 -0400 @@ -0,0 +1,90 @@ + + IDBA-UD - Iterative de Bruijn Graph Assembler for sequencing data with highly uneven depth. + + + idba_ud + + --read $read + + #if $long_read: + + --long_read $long_read + + #end if + + #if $read_level_2: + + --read_level_2 $read_level_2 + + #end if + + #if $read_level_3: + + --read_level_3 $read_level_3 + + #end if + + #if $read_level_4: + + --read_level_4 $read_level_4 + + #end if + + #if $read_level_5: + + --read_level_5 $read_level_5 + + #end if + + --mink $mink --maxk $maxk $step --inner_mink $inner_mink --inner_step $inner_step --prefix $prefix --min_count $min_count --min_support $min_support --num_threads $num_threads --seed_kmer $seed_kmer --min_contig $min_contig --similar $similar --max_mismatch $max_mismatch --min_pairs $min_pairs + + #if str( $other ) != "None": + + $other + + #end if + + ; + + mv out/scaffold.fa $output + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +