Repository revision
16:17f911830a8c

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

ivar consensus tool metadata
Miscellaneous
Call consensus from aligned BAM file
ivar_consensus
toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.2+galaxy0
1.4.2+galaxy0
ivar version | grep version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.2+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.0+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.3.2+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.3.1+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.3.1+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.3.1+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.1+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.0.1+galaxy0
ivar_consensus
Requirements (dependencies defined in the <requirements> tag set)
name version type
ivar 1.4.2 package
python 3.11.0 package
samtools 1.16.1 package
Additional information about this tool
#import re
        #set $clean_name = re.sub('[^\w\-]', '_', str($input_bam.element_identifier))
        ln -s '$input_bam' sorted.bam &&
        samtools mpileup -A -a -d 0 -Q 0 sorted.bam | ivar consensus
        -p consensus
        -q $min_qual
        -t $min_freq
        -c $min_indel_freq
        -m $min_depth
        $depth_action
        &&
        sed -i "s|consensus|$clean_name|" consensus.fa
    
None
False
Functional tests
name inputs outputs required files
Test-1 input_bam: covid19/PC00101P_sub.trimmed.sorted.bam
name: value
covid19/PC00101P_sub.trimmed.sorted.bam
value