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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo commit c6f72da672e92592f8d389375e0db84676d539a6
author iuc
date Mon, 18 Dec 2017 10:10:40 -0500
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-1:000000000000 0:478cb0b3b31a
1 <tool id="ococo" name="ococo" version="0.1.2.6" >
2 <description>consensus caller on SAM/BAM</description>
3 <requirements>
4 <requirement type="package" version="0.1.2.6">ococo</requirement>
5 </requirements>
6 <command detect_errors="exit_code">
7 <![CDATA[
8 ococo -i '$input_alignment'
9 #if $fasta_reference:
10 --fasta-ref '$fasta_reference'
11 #end if
12 --counters $counters
13 --strategy $strategy
14 --min-MQ $min_mq
15 --min-BQ $min_bq
16 --ref-weight $ref_weight
17 --min-cov $min_cov
18 --maj-thres $maj_thres
19 #for $out in str($save_output).split(','):
20 #if str($out) == 'vcf':
21 --vcf-cons $vcf_cons
22 #elif str($out) == 'fasta':
23 --fasta-cons $fasta_cons
24 #elif str($out) == 'pileup':
25 --pileup $pileup
26 #end if
27 #end for
28 ]]>
29 </command>
30 <inputs>
31 <param name="input_alignment" type="data" format="bam,sam" label="SAM/BAM dataset"/>
32 <param name="fasta_reference" type="data" format="fasta" label="Select fasta reference" optional="True"/>
33 <param name="counters" type="select" label="Counter configuration: [ococo16]">
34 <option value="ococo16">ococo16 (3b/counter, 16b/position)</option>
35 <option value="ococo32">ococo32 (7b/counter, 32b/position)</option>
36 <option value="ococo64">ococo64 (15b/counter, 64b/position)</option>
37 </param>
38 <param name="strategy" type="select" label="Strategy for updates: [majority]">
39 <option value="majority">Majority (update to majority base)</option>
40 <option value="stochastic">stochastic (update to stochastically drawn base)</option>
41 </param>
42
43 <param name="save_output" type="select" label="Save output(s)" optional="False" multiple="True" help="Determine which output file(s) to keep">
44 <option value="vcf">Consensus VCF</option>
45 <option value="fasta">Consensus Fasta</option>
46 <option value="pileup">Pileup</option>
47 </param>
48
49 <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"/>
50 <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"/>
51 <param name="ref_weight" type="integer" label="Initial nucleotides counter" help="initial counter value for nucleotides from ref [0]" value="0" argument='--ref-weight'/>
52 <param name="min_cov" type="integer" label="Minimum coverage required" help="minimum coverage required for update [2]" value="2" argument="--min-cov"/>
53 <param name="maj_thres" type="float" label="Majority consensus threshold [0.51]" value="0.51" argument="--maj-thres"/>
54 </inputs>
55
56 <outputs>
57 <data name="vcf_cons" format="vcf" label="VCF Consensus on ${input_alignment.name}">
58 <filter>'vcf' in save_output</filter>
59 </data>
60 <data name="fasta_cons" format="fasta" label="Fasta Consensus on ${input_alignment.name}">
61 <filter>'fasta' in save_output</filter>
62 </data>
63 <data name="pileup" format="pileup" label="Pileup on ${input_alignment.name}">
64 <filter>'pileup' in save_output</filter>
65 </data>
66 </outputs>
67 <tests>
68 <test>
69 <param name="input_alignment" value="alignment_A_2.sam"/>
70 <param name="fasta_reference" value="reference.fa"/>
71 <param name="save_output" value="vcf,fasta,pileup"/>
72 <output name="fasta_cons" value="answer.fa"/>
73 <output name="pileup" value="answer.pileup"/>
74 <output name="vcf_cons">
75 <assert_contents>
76 <has_text text="AF=1.00;CS=2,0,0,0;COV=2"/>
77 </assert_contents>
78 </output>
79 </test>
80 </tests>
81 <help>
82 <![CDATA[
83
84 **OCOCO - Online Consensus Caller**
85
86 OCOCO is a online consensus caller, capable to infer SNVs dynamically as read alignments are fed in.
87 OCOCO inputs unsorted alignments from an unsorted SAM/BAM stream and decides about single-nucleotide
88 updates of the current genomic consensus using statistics stored in compact several-bits counters.
89 Updates are reported in the online fashion using unsorted VCF. OCOCO provides a fast and
90 memory-efficient alternative to the usual variant calling, particularly advantageous when reads
91 are sequenced or mapped progressively, or when available computational resources are at a premium.
92
93 ]]>
94 </help>
95 <citations>
96 <citation type="bibtex">
97 @misc{1207.3907,
98 Author = {Karel Brinda},
99 Title = {Ococo: an online consensus caller},
100 Year = {2017},
101 Eprint = {arXiv:1712.01146},
102 url = {https://arxiv.org/abs/1712.01146}
103 }
104 </citation>
105 </citations>
106 </tool>