# HG changeset patch
# User bgruening
# Date 1674582399 0
# Node ID 2061fb3b81b4a1b0e4d0311dc42b089a82adaa7a
# Parent c388a21dcbf1d0aa58ccdb362e5172c5249d95da
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
diff -r c388a21dcbf1 -r 2061fb3b81b4 hifiasm.xml
--- a/hifiasm.xml Fri Jan 20 22:27:43 2023 +0000
+++ b/hifiasm.xml Tue Jan 24 17:46:39 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
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