Repository revision
8:e84073b420a8

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

khmer: Normalize By Median tool metadata
Miscellaneous
Filter reads using digital normalization via k-mer abundances
khmer_normalize_by_median
toolshed.g2.bx.psu.edu/repos/iuc/khmer_normalize_by_median/khmer_normalize_by_median/3.0.0a3+galaxy2
3.0.0a3+galaxy2
normalize-by-median.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_normalize_by_median/khmer_normalize_by_median/3.0.0a3+galaxy2 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/khmer_normalize_by_median/khmer_normalize_by_median/3.0.0a3+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/khmer_normalize_by_median/khmer_normalize_by_median/3.0.0a1.0
toolshed.g2.bx.psu.edu/repos/iuc/khmer_normalize_by_median/khmer_normalize_by_median/2.0.0
khmer_normalize_by_median
Requirements (dependencies defined in the <requirements> tag set)
name version type
khmer 3.0.0a3 package
Additional information about this tool
#import re
set -u &&
mkdir output &&



#import re
mkdir input/ &&
#set gzip=""
#for $num, $input in enumerate($inputs)
    ln -s '${input}' 'input/$re.sub("[^\w\-_.]", "_", $input.element_identifier).$input.ext' &&
    #if str($input).endswith(".gz"):
        #set gzip="--gzip"
    #end if
#end for
cd output/ &&
normalize-by-median.py
${paired_switch}
${force_single_switch}


#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

    
--cutoff=${cutoff}
#if $unpaired_reads_filename
    --unpaired-reads=${unpaired_reads_filename}
#end if
#if $save_countgraph
    --savegraph=${countgraph}
#end if
#if $countgraph_to_load
    --loadgraph=${countgraph_to_load}
#end if
--report=${report}
$gzip


#for $num, $input in enumerate($inputs)
    '../input/$re.sub("[^\w\-_.]", "_", $input.element_identifier).$input.ext'
#end for

    
None
False
Functional tests
name inputs outputs required files
Test-1 inputs: test-abund-read-2.fa
cutoff: 1
parameters|ksize: 17
parameters|type: specific
name: value
test-abund-read-2.fa
value
Test-2 inputs: test-abund-read-2.fa.gz
cutoff: 2
parameters|ksize: 17
parameters|type: specific
name: value
test-abund-read-2.fa.gz
value
Test-3 inputs: test-abund-read-paired.fa
cutoff: 1
parameters|ksize: 17
parameters|type: specific
name: value
test-abund-read-paired.fa
value