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| author | jowong |
|---|---|
| date | Mon, 26 Nov 2018 02:14:27 -0500 |
| parents | 69d52f45c2fa |
| children | ab0f91be3a90 |
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<tool id="khmer_load_into_counting" name="Load Into Counting" version="1.0.5"> <description>Creates k-mer countgraph using reads</description> <requirements> <requirement type="package" version="2.1.2">khmer</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ load-into-counting.py $advanced.b $advanced.small -k $kmer -U $advanced.ukmer #if str( $advanced.max_mem ) != "0" -M $advanced.max_mem #end if #if str( $advanced.fp_rate ) != "0" --fp-rate $advanced.fp_rate #end if -N $advanced.num_table -x $advanced.table_size hash.ct.gz #if str( $data_input.data_selector ) == "paired" $data_input.input1.forward $data_input.input1.reverse #end if #if str( $data_input.data_selector ) == "single" $data_input.input2 #end if ]]></command> <inputs> <conditional name="data_input"> <param name="data_selector" type="select" label="Single or Paired-end Data" help="Select between paired and single end data to add name to dataset"> <option value="paired">Paired</option> <option value="single">Single</option> </param> <when value="paired"> <param name="input1" format="data" type="data_collection" collection_type="paired" label="Select a paired collection" help="a paired data"/> </when> <when value="single"> <param name="input2" format="data" type="data" label="input" help="Specify dataset with single reads"/> </when> </conditional> <param name="kmer" type="integer" value="32" label="K-mer" help="K-mer size to use (default: 32)" /> <section name="advanced" title="Advanced options" expanded="false"> <param type="boolean" argument="--small" label="Small count" checked="false" truevalue="--small-count" falsevalue="" help="Reduce memory usage by using a smaller counter for individual kmers. (default: False)"/> <param type="boolean" argument="-b" label="big count" checked="True" truevalue="-b" falsevalue="--no-bigcount" help="Reduce memory usage by using a smaller counter for individual kmers. (default: True)"/> <param name="thread" type="integer" value="1" label="Threads" help="Number of simultaneous threads to execute (default: 1)" /> <param name="ukmer" type="integer" value="0" label="Unique K-mer" help="approximate number of unique kmers in the input set (default: 0)" /> <param name="num_table" type="integer" value="1" label="Number of tables" help="number of tables to use (default: False)" /> <param name="table_size" type="integer" value="1000000000" label="Maximum size of table" help="maximum size of tables to use (default: False)" /> <param name="max_mem" type="integer" value="0" label="Maximum Memory" help="number of tables to use (default: False)" /> <param name="fp_rate" type="integer" value="0" label="FP rate override" help="Override the automatic FP rate setting for the current script" /> </section> </inputs> <outputs> <data name="hash_output" label="Hash output" format="data" from_work_dir="hash.ct.gz"/> </outputs> <help><![CDATA[ || This is the script load-into-counting.py in khmer. || You are running khmer version 2.1.2 || You are also using screed version 1.0 || || If you use this script in a publication, please cite EACH of the following: || || * MR Crusoe et al., 2015. http://dx.doi.org/10.12688/f1000research.6924.1 || * Q Zhang et al., http://dx.doi.org/10.1371/journal.pone.0101271 || * A. Döring et al. http://dx.doi.org:80/10.1186/1471-2105-9-11 || || Please see http://khmer.readthedocs.io/en/latest/citations.html for details. usage: load-into-counting.py [--version] [--info] [-h] [-k KSIZE] [-U UNIQUE_KMERS] [--fp-rate FP_RATE] [-M MAX_MEMORY_USAGE] [--small-count] [-T THREADS] [-b] [-s FORMAT] [-f] [-q] output_countgraph_filename input_sequence_filename [input_sequence_filename ...] Build a k-mer countgraph from the given sequences. positional arguments: output_countgraph_filename The name of the file to write the k-mer countgraph to. input_sequence_filename The names of one or more FAST[AQ] input sequence files. optional arguments: --version show program's version number and exit --info print citation information -h, --help show this help message and exit -k KSIZE, --ksize KSIZE k-mer size to use (default: 32) -U UNIQUE_KMERS, --unique-kmers UNIQUE_KMERS approximate number of unique kmers in the input set (default: 0) --fp-rate FP_RATE Override the automatic FP rate setting for the current script (default: None) -M MAX_MEMORY_USAGE, --max-memory-usage MAX_MEMORY_USAGE maximum amount of memory to use for data structure (default: None) --small-count Reduce memory usage by using a smaller counter for individual kmers. (default: False) -T THREADS, --threads THREADS Number of simultaneous threads to execute (default: 1) -b, --no-bigcount The default behaviour is to count past 255 using bigcount. This flag turns bigcount off, limiting counts to 255. (default: True) -s FORMAT, --summary-info FORMAT What format should the machine readable run summary be in? (`json` or `tsv`, disabled by default) (default: None) -f, --force Overwrite output file if it exists (default: False) -q, --quiet Note: with `-b`/`--no-bigcount` the output will be the exact size of the k-mer countgraph and this script will use a constant amount of memory. In exchange k-mer counts will stop at 255. The memory usage of this script with `-b` will be about 1.15x the product of the `-x` and `-N` numbers. Example: load-into-counting.py -k 20 -x 5e7 out data/100k-filtered.fa Multiple threads can be used to accelerate the process, if you have extra cores to spare. Example: load-into-counting.py -k 20 -x 5e7 -T 4 out data/100k-filtered.fa ]]></help> <citations> <citation type="bibtex"> @misc{githubkhmer, author = {Crusoe, Michael}, year = {2015}, title = {khmer}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/dib-lab/khmer}, }</citation> </citations> </tool>