Mercurial > repos > iuc > ococo
changeset 0:03cabb6711c5 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo commit c6f72da672e92592f8d389375e0db84676d539a6
| author | iuc |
|---|---|
| date | Mon, 18 Dec 2017 10:11:02 -0500 |
| parents | |
| children | |
| files | ococo.xml test-data/alignment_A_2.sam test-data/answer.fa test-data/answer.pileup test-data/reference.fa |
| diffstat | 5 files changed, 115 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ococo.xml Mon Dec 18 10:11:02 2017 -0500 @@ -0,0 +1,106 @@ +<tool id="ococo" name="ococo" version="0.1.2.6" > + <description>consensus caller on SAM/BAM</description> + <requirements> + <requirement type="package" version="0.1.2.6">ococo</requirement> + </requirements> + <command detect_errors="exit_code"> +<![CDATA[ + ococo -i '$input_alignment' + #if $fasta_reference: + --fasta-ref '$fasta_reference' + #end if + --counters $counters + --strategy $strategy + --min-MQ $min_mq + --min-BQ $min_bq + --ref-weight $ref_weight + --min-cov $min_cov + --maj-thres $maj_thres + #for $out in str($save_output).split(','): + #if str($out) == 'vcf': + --vcf-cons $vcf_cons + #elif str($out) == 'fasta': + --fasta-cons $fasta_cons + #elif str($out) == 'pileup': + --pileup $pileup + #end if + #end for +]]> + </command> + <inputs> + <param name="input_alignment" type="data" format="bam,sam" label="SAM/BAM dataset"/> + <param name="fasta_reference" type="data" format="fasta" label="Select fasta reference" optional="True"/> + <param name="counters" type="select" label="Counter configuration: [ococo16]"> + <option value="ococo16">ococo16 (3b/counter, 16b/position)</option> + <option value="ococo32">ococo32 (7b/counter, 32b/position)</option> + <option value="ococo64">ococo64 (15b/counter, 64b/position)</option> + </param> + <param name="strategy" type="select" label="Strategy for updates: [majority]"> + <option value="majority">Majority (update to majority base)</option> + <option value="stochastic">stochastic (update to stochastically drawn base)</option> + </param> + + <param name="save_output" type="select" label="Save output(s)" optional="False" multiple="True" help="Determine which output file(s) to keep"> + <option value="vcf">Consensus VCF</option> + <option value="fasta">Consensus Fasta</option> + <option value="pileup">Pileup</option> + </param> + + <param name="min_mq" type="integer" label="Minimum mapping quality score" help="skip alignments with mapping quality smaller than INT [1]" value="1" argument="min-MQ"/> + <param name="min_bq" type="integer" label="Minimum base quality score" help="skip bases with base quality smaller than INT [13]" value="13" argument="--min-BQ"/> + <param name="ref_weight" type="integer" label="Initial nucleotides counter" help="initial counter value for nucleotides from ref [0]" value="0" argument='--ref-weight'/> + <param name="min_cov" type="integer" label="Minimum coverage required" help="minimum coverage required for update [2]" value="2" argument="--min-cov"/> + <param name="maj_thres" type="float" label="Majority consensus threshold [0.51]" value="0.51" argument="--maj-thres"/> + </inputs> + + <outputs> + <data name="vcf_cons" format="vcf" label="VCF Consensus on ${input_alignment.name}"> + <filter>'vcf' in save_output</filter> + </data> + <data name="fasta_cons" format="fasta" label="Fasta Consensus on ${input_alignment.name}"> + <filter>'fasta' in save_output</filter> + </data> + <data name="pileup" format="pileup" label="Pileup on ${input_alignment.name}"> + <filter>'pileup' in save_output</filter> + </data> + </outputs> + <tests> + <test> + <param name="input_alignment" value="alignment_A_2.sam"/> + <param name="fasta_reference" value="reference.fa"/> + <param name="save_output" value="vcf,fasta,pileup"/> + <output name="fasta_cons" value="answer.fa"/> + <output name="pileup" value="answer.pileup"/> + <output name="vcf_cons"> + <assert_contents> + <has_text text="AF=1.00;CS=2,0,0,0;COV=2"/> + </assert_contents> + </output> + </test> + </tests> + <help> +<![CDATA[ + +**OCOCO - Online Consensus Caller** + +OCOCO is a online consensus caller, capable to infer SNVs dynamically as read alignments are fed in. +OCOCO inputs unsorted alignments from an unsorted SAM/BAM stream and decides about single-nucleotide +updates of the current genomic consensus using statistics stored in compact several-bits counters. +Updates are reported in the online fashion using unsorted VCF. OCOCO provides a fast and +memory-efficient alternative to the usual variant calling, particularly advantageous when reads +are sequenced or mapped progressively, or when available computational resources are at a premium. + +]]> + </help> + <citations> + <citation type="bibtex"> + @misc{1207.3907, + Author = {Karel Brinda}, + Title = {Ococo: an online consensus caller}, + Year = {2017}, + Eprint = {arXiv:1712.01146}, + url = {https://arxiv.org/abs/1712.01146} + } + </citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignment_A_2.sam Mon Dec 18 10:11:02 2017 -0500 @@ -0,0 +1,4 @@ +@HD VN:1.5 SO:coordinate +@SQ SN:seq LN:2 +read_1 0 seq 2 42 1M * 0 0 A * +read_2 0 seq 2 42 1M * 0 0 A * \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/answer.fa Mon Dec 18 10:11:02 2017 -0500 @@ -0,0 +1,2 @@ +>seq +NA