Repository revision
3:920677cd220f

Repository 'velvet'
hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/velvet

velvetg tool metadata
Miscellaneous
velvetg
Velvet sequence assembler for very short reads
velvetg
toolshed.g2.bx.psu.edu/repos/devteam/velvet/velvetg/1.2.10.2
1.2.10.2
velvetg 2>&1 | grep "Version" | sed -e 's/Version //'
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/devteam/velvet/velvetg/1.2.10.2 (this tool)
toolshed.g2.bx.psu.edu/repos/devteam/velvet/velvetg/1.2.10.1
toolshed.g2.bx.psu.edu/repos/devteam/velvet/velvetg/1.2.10.0
velvetg
Requirements (dependencies defined in the <requirements> tag set)
name version type
velvet 1.2.10 package
Additional information about this tool
ln -s '$input.extra_files_path'/Roadmaps &&
    ln -s '$input.extra_files_path'/Sequences &&
    velvetg .
           #if 'amos' in $add_out:
               -amos_file yes
           #end if
           #if 'unused' in $add_out:
               -unused_reads yes
           #end if
           $read_trkg
           #if $coverage.cutoff == "auto":
               -cov_cutoff auto
           #elif $coverage.cutoff == "value":
               -cov_cutoff $coverage.cov_cutoff
           #end if
           #if $expected.coverage == "auto":
               -exp_cov auto
           #elif $expected.coverage == "value":
               -exp_cov $expected.exp_cov
           #end if
           #if $contig_lgth.use_contig_lgth == "yes":
               -min_contig_lgth $contig_lgth.min_contig_lgth
           #end if
           #if $reads.paired == "yes":
               #if int($reads.ins_length) > 0:
                   -ins_length $reads.ins_length
               #end if
               #if $reads.options.advanced == "yes":
                   #if int($reads.options.ins_length_sd) > 0:
                       -ins_length_sd $reads.options.ins_length_sd
                   #end if
                   #if int($reads.options.ins_length2) > 0:
                       -ins_length2 $reads.options.ins_length2
                   #end if
                   #if int($reads.options.ins_length2_sd) > 0:
                       -ins_length2_sd $reads.options.ins_length2_sd
                   #end if
                   #if int($reads.options.ins_length3) > 0:
                       -ins_length3 $reads.options.ins_length3
                   #end if
                   #if int($reads.options.ins_length3_sd) > 0:
                       -ins_length3_sd $reads.options.ins_length3_sd
                   #end if
                   #if int($reads.options.ins_length4) > 0:
                       -ins_length4 $reads.options.ins_length4
                   #end if
                   #if int($reads.options.ins_length4_sd) > 0:
                       -ins_length4_sd $reads.options.ins_length4_sd
                   #end if
                   #if int($reads.options.ins_length_long) > 0:
                       -ins_length_long $reads.options.ins_length_long
                   #end if
                   #if int($reads.options.ins_length_long_sd) > 0:
                       -ins_length_long_sd $reads.options.ins_length_long_sd
                   #end if
                   #if int($reads.options.max_branch_length) > 0:
                       -max_branch_length $reads.options.max_branch_length
                   #end if
                   #if int($reads.options.max_divergence) > 0:
                       -max_divergence $reads.options.max_divergence
                   #end if
                   #if int($reads.options.max_gap_count) > 0:
                       -max_gap_count $reads.options.max_gap_count
                   #end if
                   #if int($reads.options.min_pair_count) > 0:
                       -min_pair_count $reads.options.min_pair_count
                   #end if
                   #if int($reads.options.max_coverage) > 0:
                       -max_coverage $reads.options.max_coverage
                   #end if
                   #if int($reads.options.long_mult_cutoff) > 0:
                       -long_mult_cutoff $reads.options.long_mult_cutoff
                   #end if
                   $reads.options.scaffolding
               #end if
           #end if
  
None
False
Functional tests
name inputs outputs required files
Test-1 input: velvetg_paired.out
coverage|cutoff: auto
read_trkg: False
contig_lgth|use_contig_lgth: no
expected|coverage: auto
add_out: ['amos', 'unused', 'lastgraph']
reads|paired: no
name: value
name: value
name: value
name: value
name: value
velvetg_paired.out
value