Mercurial > repos > iuc > ococo

annotate ococo.xml @ 0:478cb0b3b31a draft default tip

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