Repository revision
5:aa35ee7f3ab2

Repository 'lofreq_viterbi'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi

Realign reads tool metadata
Miscellaneous
with LoFreq viterbi
lofreq_viterbi
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
2.1.5+galaxy0
lofreq version | grep version | cut -d ' ' -f 2
True
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
    
None
False
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