| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.20+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13 |
| toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.3.1.1 |
| toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.3.1 |
| racon |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| racon | 1.5.0 | package |
| Additional information about this tool |
#if $reads.ext.startswith("fasta")
#set ext="fasta"
#else
#set ext="fastq"
#end if
#if $reads.ext.endswith(".gz")
#set ext=ext+".gz"
#end if
ln -s '$reads' reads.$ext &&
#if $overlaps.ext == 'sam':
ln -s '$overlaps' overlaps.${overlaps.ext} &&
#else:
ln -s '$overlaps' overlaps.paf &&
#end if
#if $corrected_reads.ext.startswith("fasta")
#set cext="fasta"
#else
#set cext="fastq"
#end if
#if $corrected_reads.ext.endswith(".gz")
#set cext=cext+".gz"
#end if
ln -s '$corrected_reads' corrected_reads.$cext &&
racon
reads.$ext
#if $overlaps.ext == 'sam':
overlaps.${overlaps.ext}
#else:
overlaps.paf
#end if
corrected_reads.$cext
-t \${GALAXY_SLOTS:-4}
$include_unpolished
$fragment_correction
-w $window_length
-q $quality_threshold
-e $error_threshold
$no_trimming
-m $match
-x $mismatch
-g $gap
> racon_polished_consensus.fa
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
reads: sample_reads.fasta overlaps: sample_overlaps.sam corrected_reads: sample_layout.fasta include_unpolished: True fragment_correction: True window_length: 800 error_threshold: 0.2 |
name: value |
sample_reads.fasta sample_overlaps.sam sample_layout.fasta value |
| Test-2 |
reads: sample_reads.fasta overlaps: sample_overlaps.paf corrected_reads: sample_layout.fasta |
name: value |
sample_reads.fasta sample_overlaps.paf sample_layout.fasta value |
| Test-3 |
reads: sample_reads.fasta overlaps: sample_overlaps.sam corrected_reads: sample_layout.fasta include_unpolished: False fragment_correction: False quality_threshold: 9.0 no_trimming: True match: 7 mismatch: -4 gap: -3 |
name: value |
sample_reads.fasta sample_overlaps.sam sample_layout.fasta value |