Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.4+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.3.1+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.3.1+galaxy0 |
lofreq_viterbi |
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 viterbi --ref '$reference_fasta_fn' ${adv_options.keepflags} --defqual ${adv_options.bq2_handling.defqual} --out tmp.bam '$reads' && samtools sort --no-PG -T "\${TMPDIR:-.}" -@ \${GALAXY_SLOTS:-1} -O BAM -o '$realigned' tmp.bam
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 adv_options|keepflags: True |
name: value |
lofreq-in1.bam pBR322.fa value |