# HG changeset patch # User bgruening # Date 1674582374 0 # Node ID 60b0eaaece5fa9d95234bcd04eeca00683a1cb0c # Parent ec4cd51e90b0e0a745fd633b20c662b14bea2ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa diff -r ec4cd51e90b0 -r 60b0eaaece5f hifiasm.xml --- a/hifiasm.xml Fri Jan 20 22:27:21 2023 +0000 +++ b/hifiasm.xml Tue Jan 24 17:46:14 2023 +0000 @@ -2,7 +2,7 @@ haplotype-resolved de novo assembler for PacBio Hifi reads 0.18.5 - 0 + 1 fasta,fasta.gz,fastq,fastq.gz @@ -21,6 +21,7 @@ #set $hap2_inputs = list() #set $hic1_inputs = list() #set $hic2_inputs = list() + #set $ultralong_inputs = list() #for idx, read in enumerate($mode.reads): #set $inputfile = 'input_%d.%s' % ($idx, $read.dataset.extension) ln -s '$read' $inputfile && @@ -40,6 +41,14 @@ $hic2_inputs.append($inputfile) #end for #end if + #if str($ont_integration.ont_integration_selector) == 'set' + mkdir ultralong && + #for idx, read in enumerate($ont_integration.ul): + #set $inputfile = './ultralong/input_%d.%s' % ($idx, $read.dataset.extension) + ln -s '$read' $inputfile && + $ultralong_inputs.append($inputfile) + #end for + #end if #if str($mode.mode_selector) == 'trio': #for idx, read in enumerate($mode.hap1_reads): #set $inputfile = 'hap1_input_%d.%s' % ($idx, $read.dataset.extension) @@ -108,8 +117,8 @@ #end if #if str($hic_partition.hic_partition_selector) == 'set': - --h1 '${ ' '.join(["%s" % $x for $x in $hic1_inputs]) }' - --h2 '${ ' '.join(["%s" % $x for $x in $hic2_inputs]) }' + --h1 ${ ' '.join(["'%s'" % $x for $x in $hic1_inputs]) } + --h2 ${ ' '.join(["'%s'" % $x for $x in $hic2_inputs]) } #if $hic_partition.seed: --seed $hic_partition.seed #end if @@ -125,6 +134,16 @@ --l-msjoin $hic_partition.l_msjoin #end if + #if str($ont_integration.ont_integration_selector) == 'set': + --ul ${ ' '.join(["'%s'" % $x for $x in $ultralong_inputs]) } + #if $ont_integration.ul_rate: + --ul-rate $ont_integration.ul_rate + #end if + #if $ont_integration.ul_tip: + --ul-tip $ont_integration.ul_tip + #end if + #end if + ## Changed the default outputs of hifiasm. Hifiasm outputs a primary assembly and two balanced haplotypes in default. Incorporated the option '--primary' to output primary assembly and alternate assembly. --primary $input_filenames @@ -207,6 +226,18 @@ + + + + + + + + + + + + @@ -298,6 +329,7 @@ + @@ -306,6 +338,7 @@ + @@ -314,7 +347,7 @@ - + @@ -329,7 +362,7 @@ - + @@ -364,7 +397,7 @@ - + @@ -381,7 +414,7 @@ - + @@ -394,7 +427,7 @@ - + @@ -407,7 +440,7 @@ - + @@ -420,7 +453,7 @@ - + @@ -433,7 +466,7 @@ - + @@ -446,7 +479,7 @@ - + @@ -459,6 +492,19 @@ + + + + + + + + + + + + +