| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.4+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.3.1+galaxy0 |
| lofreq_alnqual |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| lofreq | 2.1.5 | package |
| Additional information about this tool |
#if str($reference_source.ref_selector) == 'history':
#set $reference_fasta_fn = 'reference.fa'
ln -s '$reference_source.ref' $reference_fasta_fn &&
lofreq faidx $reference_fasta_fn 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&
#else
#set $reference_fasta_fn = str($reference_source.ref.fields.path)
#end if
lofreq alnqual -b ${alnqual_choice.extended_baq} ${alnqual_choice.alnquals_to_use} $recompute_all '$reads' '$reference_fasta_fn' > '$output'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
reads: lofreq-in1.bam reference_source|ref: pBR322.fa reference_source|ref_selector: history |
name: value |
lofreq-in1.bam pBR322.fa value |
| Test-2 |
reads: lofreq-in1.bam reference_source|ref: pBR322.fa reference_source|ref_selector: history alnqual_choice|alnquals_to_use: -B |
name: value |
lofreq-in1.bam pBR322.fa value |
| Test-3 |
reads: lofreq-in1.bam reference_source|ref: pBR322.fa reference_source|ref_selector: history alnqual_choice|alnquals_to_use: -A |
name: value |
lofreq-in1.bam pBR322.fa value |
| Test-4 |
reads: lofreq-in1.bam reference_source|ref: pBR322.fa reference_source|ref_selector: history alnqual_choice|extended_baq: False |
name: value |
lofreq-in1.bam pBR322.fa value |
| Test-5 |
reads: lofreq-in1.bam reference_source|ref: pBR322.fa reference_source|ref_selector: history |
name: value |
lofreq-in1.bam pBR322.fa value |