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 |