Repository revision
8:c018a72b523e

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

khmer: Abundance Distribution (all-in-one) tool metadata
Miscellaneous
Calculate abundance distribution of k-mers
khmer_abundance_distribution_single
toolshed.g2.bx.psu.edu/repos/iuc/khmer_abundance_distribution_single/khmer_abundance_distribution_single/3.0.0a3+galaxy2
3.0.0a3+galaxy2
abundance-dist-single.py --version 2>&1 | tail -n 1 | cut -d ' ' -f 2
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/khmer_abundance_distribution_single/khmer_abundance_distribution_single/3.0.0a3+galaxy2 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/khmer_abundance_distribution_single/khmer_abundance_distribution_single/3.0.0a3+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/khmer_abundance_distribution_single/khmer_abundance_distribution_single/3.0.0a1.0
toolshed.g2.bx.psu.edu/repos/iuc/khmer_abundance_distribution_single/khmer_abundance_distribution_single/2.0.0
khmer_abundance_distribution_single
Requirements (dependencies defined in the <requirements> tag set)
name version type
khmer 3.0.0a3 package
Additional information about this tool
set -u &&
abundance-dist-single.py


#if $parameters.type == "simple"
  --ksize=20
  --n_tables=4
  --max-tablesize=$parameters.tablesize
#else
  --ksize=$parameters.ksize
  --n_tables=$parameters.n_tables
  --max-tablesize="$parameters.tablesize_specific"
#end if

    
${zero}
${bigcount}
#if $save_countgraph
    --savegraph=${optional_output_countgraph}
#end if
--squash
--threads \${GALAXY_SLOTS:-4}
${input_sequence_filename}
${output_histogram_filename}


    
None
False
Functional tests
name inputs outputs required files
Test-1 input_sequence_filename: test-abund-read-2.fa
parameters|ksize: 17
parameters|n_tables: 2
parameters|tablesize_specific: 1e7
parameters|type: specific
name: value
test-abund-read-2.fa
value
Test-2 input_sequence_filename: test-abund-read-2.fq.gz
bigcount: False
parameters|ksize: 17
parameters|n_tables: 2
parameters|tablesize_specific: 1e7
parameters|type: specific
name: value
test-abund-read-2.fq.gz
value