| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxy-australia/hifiasm_meta/hifiasm_meta/0.3.1+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxy-australia/hifiasm_meta/hifiasm_meta/0.3+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/galaxy-australia/hifiasm_meta/hifiasm_meta/hamtv0.3+galaxy0 |
| hifiasm_meta |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| hifiasm_meta | hamtv0.3.1 | package |
| Additional information about this tool |
##################
## SET UP FILES ##
##################
#set reads_fn = 'reads.' + $reads.ext
ln -s '$reads' '$reads_fn' &&
#################
## RUN HIFIASM ##
#################
hifiasm_meta
## bloom filter parameter
#if $f:
-f '$f'
#end if
## read selection parameters
#if $read_selection.forced_read_selection.force_rs == "yes":
--force-rs
--lowq-10 '$read_selection.forced_read_selection.lowq_10'
--lowq-3 '$read_selection.forced_read_selection.lowq_3'
--lowq-5 '$read_selection.forced_read_selection.lowq_5'
#else
$read_selection.forced_read_selection.S
#end if
-a '$assembly.a'
-k '$overlap_correction.k'
-o asm
-r '$overlap_correction.r'
-t \${GALAXY_SLOTS:-4}
'$reads_fn'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
reads: zymoD6331std-ecoli-ten-percent.42.1.fq.gz f: 0 |
zymoD6331std-ecoli-ten-percent.42.1.fq.gz |
|
| Test-2 |
reads: tiny.fa.gz f: 0 read_selection|forced_read_selection|force_rs: yes |
tiny.fa.gz |
|
| Test-3 |
reads: zymoD6331std-ecoli-ten-percent.42.1.fq.gz f: 0 read_selection|forced_read_selection|S: True read_selection|forced_read_selection|force_rs: no |
zymoD6331std-ecoli-ten-percent.42.1.fq.gz |