# HG changeset patch # User iuc # Date 1742839821 0 # Node ID 5d365d5cbe9ded415171792fde3340faa47fa1c2 # Parent 170061c052ad50faebcd94e1549e8f5fb105a5ee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit ed3c07cc67bacb7c1c5a929d5f427536a35db5ca diff -r 170061c052ad -r 5d365d5cbe9d hifiasm.xml --- a/hifiasm.xml Mon Mar 10 08:09:25 2025 +0000 +++ b/hifiasm.xml Mon Mar 24 18:10:21 2025 +0000 @@ -1,7 +1,7 @@ haplotype-resolved de novo assembler for PacBio Hifi reads - 0.24.0 + 0.25.0 0 fasta,fasta.gz,fastq,fastq.gz @@ -72,6 +72,9 @@ #end if #end if hifiasm + #if str($mode.mode_selector) == 'ont': + --ont + #end if -t \${GALAXY_SLOTS:-1} -o output -f $filter_bits @@ -88,6 +91,8 @@ #if $advanced_options.hg_size --hg-size $advanced_options.hg_size #end if + --rl-cut $advanced_options.rl_cut + --sc-cut $advanced_options.sc_cut #end if #if str($assembly_options.assembly_selector) == 'set': @@ -181,11 +186,15 @@ + + + + @@ -303,6 +312,8 @@ [0-9kKmMGg]+ + + @@ -319,18 +330,18 @@ - + - mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank' + mode['mode_selector'] != 'trio' and hic_partition['hic_partition_selector'] == 'blank' - mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank' + mode['mode_selector'] != 'trio' and hic_partition['hic_partition_selector'] == 'blank' - mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank' + mode['mode_selector'] != 'trio' and hic_partition['hic_partition_selector'] == 'blank' - mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank' + mode['mode_selector'] != 'trio' and hic_partition['hic_partition_selector'] == 'blank' @@ -347,19 +358,19 @@ - mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set' + mode['mode_selector'] != 'trio' and hic_partition['hic_partition_selector'] == 'set' - mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set' + mode['mode_selector'] != 'trio' and hic_partition['hic_partition_selector'] == 'set' - mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set' + mode['mode_selector'] != 'trio' and hic_partition['hic_partition_selector'] == 'set' - mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set' + mode['mode_selector'] != 'trio' and hic_partition['hic_partition_selector'] == 'set' - mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set' + mode['mode_selector'] != 'trio' and hic_partition['hic_partition_selector'] == 'set' @@ -436,13 +447,13 @@ - + - + @@ -606,6 +617,15 @@ + + + + + + + + +