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comparison optitype.xml @ 3:4f78281c42ff draft

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author jjohnson
date Mon, 23 Nov 2015 09:56:42 -0500
parents 61fc10014a9e
children 111d2508ab15
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2:61fc10014a9e 3:4f78281c42ff
60 </conditional> 60 </conditional>
61 <param name="read_type" type="select" label="Nucleotide Type" help=""> 61 <param name="read_type" type="select" label="Nucleotide Type" help="">
62 <option value="--rna">RNA</option> 62 <option value="--rna">RNA</option>
63 <option value="--dna">DNA</option> 63 <option value="--dna">DNA</option>
64 </param> 64 </param>
65 <param name="beta" type="float" value="" min="0.0" max="0.1" optional="true" label="homozygosity beta" help="The beta value for for homozygosity detection"/> 65 <param name="beta" type="float" value="" min="0.0" max="0.1" optional="true" label="homozygosity beta" help="The beta value for for homozygosity detection (Leave blank for default: 0.009)"/>
66 <param name="enumerations" type="integer" value="" min="1" max="5" optional="true" label="Enumerations" help="The number of enumerations"/> 66 <param name="enumerations" type="integer" value="" min="1" max="5" optional="true" label="Enumerations" help="The number of enumerations (Leave blank for default: 1)"/>
67 <param name="outdir" type="hidden" value="output_dir"/> 67 <param name="outdir" type="hidden" value="output_dir"/>
68 </inputs> 68 </inputs>
69 <outputs> 69 <outputs>
70 <data format="pdf" name="coverage_plot" label="${tool.name} on ${on_string} coverage_plot.pdf"/> 70 <data format="pdf" name="coverage_plot" label="${tool.name} on ${on_string} coverage_plot.pdf"/>
71 <data format="tabular" name="result" label="${tool.name} on ${on_string} result.tsv"/> 71 <data format="tabular" name="result" label="${tool.name} on ${on_string} result.tsv"/>
77 <help> 77 <help>
78 <![CDATA[ 78 <![CDATA[
79 **OptiType** 79 **OptiType**
80 ============ 80 ============
81 81
82 OptiType_ is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles.
83
84 **INPUTS**
85
86 RNA or DNA sequences in fastq format.
87
88 **OPTIONS**
89
90 --beta <BETA_VALUE> The beta value for for homozygosity detection (see cited paper).
91 Default: 0.009. Handle with care.
92 --enumerate <ENUMERATIONS> Number of enumerations.
93 OptiType will output the optimal solution and the top N-1 suboptimal solutions in the results.
94 Default: 1
95
96
97 **OUTPUTS**
98
99 result.tsv A TAB-separated file of HLA genotyping predictions:
100
101 ::
102
103 A1 A2 B1 B2 C1 C2 Reads Objective
104 0 A*31:01 A*68:01 B*40:01 B*51:01 C*15:02 C*03:04 132 128.43599999999998
105
106
107 coverage_plot.pdf Plots of coverage of HLA genotyping predictions
108
109 .. _OptiType: https://github.com/FRED-2/OptiType
82 ]]> 110 ]]>
83 </help> 111 </help>
84 <citations> 112 <citations>
85 <citation type="doi">10.1093/bioinformatics/btu548. Epub 2014 Aug 20.</citation> 113 <citation type="doi">10.1093/bioinformatics/btu548</citation>
86 </citations> 114 </citations>
87 </tool> 115 </tool>