Repository revision
3:4fc0cb2ac8ae

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

Mummerplot tool metadata
Miscellaneous
Mummerplot
Generate 2-D dotplot of aligned sequences
mummer_mummerplot
toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy2
4.0.0rc1+galaxy2
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy2 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2
mummer_mummerplot
Requirements (dependencies defined in the <requirements> tag set)
name version type
mummer4 4.0.0rc1 package
gnuplot 5.4.1 package
Additional information about this tool
ln -s $reference_sequence reference.fa &&
        ln -s $query_sequence query.fa &&
        mummerplot
            -b '$breaklen'
            $color
            $coverage
            $filter
            $fat
            #if str($labels.IDs) == 'yes':
                -IdR '$labels.ref_id'
                -IdQ '$labels.query_id'
            #end if
            #if str($sequences.seq_input) == 'yes':
                -R '$reference_sequence'
                -Q '$query_sequence'
                $sequences.layout
            #end if
            -s '$size'
            -terminal png
            -title '$title'
            $snp
            #if $range.custom == 'yes':
                -x [$range.min_x:$range.max_x]
                -y [$range.min_y:$range.max_y]
            #end if
            '$delta'
            && gnuplot < out.gp
        
    
None
False
Functional tests
name inputs outputs required files
Test-1 delta: nucmer.txt
reference_sequence: human_aqp3.fasta
query_sequence: mouse_aqp3.fasta
sequences|seq_input: no
extra_outs: all
name: value
name: value
name: value
name: value
name: value
nucmer.txt
human_aqp3.fasta
mouse_aqp3.fasta
value