Repository revision
8:97f65399e30d

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

khmer: Filter reads tool metadata
Miscellaneous
by minimal k-mer abundance
khmer_filter_abundance
toolshed.g2.bx.psu.edu/repos/iuc/khmer_filter_abundance/khmer_filter_abundance/3.0.0a3+galaxy2
3.0.0a3+galaxy2
filter-abund.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_filter_abundance/khmer_filter_abundance/3.0.0a3+galaxy2 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/khmer_filter_abundance/khmer_filter_abundance/3.0.0a3+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/khmer_filter_abundance/khmer_filter_abundance/3.0.0a1.0
toolshed.g2.bx.psu.edu/repos/iuc/khmer_filter_abundance/khmer_filter_abundance/2.0.0
khmer_filter_abundance
Requirements (dependencies defined in the <requirements> tag set)
name version type
khmer 3.0.0a3 package
Additional information about this tool
set -u &&


#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($input).endswith(".gz"):
        #set gzip="--gzip"
    #end if
#end for
mkdir output && cd output &&
filter-abund.py
--cutoff=${cutoff}
${variable_coverage}
--threads \${GALAXY_SLOTS:-4}
${input_countgraph_filename}


#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
input_countgraph_filename: test-abund-read-2.oxlicg
test-abund-read-2.fa
test-abund-read-2.oxlicg
Test-2 inputs: test-abund-read-2.fa
cutoff: 1
input_countgraph_filename: test-abund-read-2.oxlicg
test-abund-read-2.fa
test-abund-read-2.oxlicg