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1 <tool id="optitype" name="OptiType" version="1.0.0">
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2 <description>HLA genotyping predictions from NGS data</description>
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3 <requirements>
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4 <requirement type="package" version="1.8.12">hdf5</requirement>
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5 <requirement type="package" version="3.4.0">razers3</requirement>
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6 <requirement type="package" version="1.0">optitype</requirement>
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7 <requirement type="package" version="2.9.5">cbc</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" level="fatal" description="Error Running optitype" />
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11 </stdio>
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12 <command>
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13 <![CDATA[
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14 #set $fastqs = []
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15 #if str( $fastq_input.fastq_input_selector ) == "paired":
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16 ln -s "${fastq_input.fastq_input1}" reads_1.fastq
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17 && ln -s "${fastq_input.fastq_input2}" reads_2.fastq
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18 #set $fastqs = ['reads_1.fastq','reads_2.fastq']
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19 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection":
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20 ln -s "${fastq_input.fastq_input1.forward}" reads_1.fastq
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21 && ln -s "${fastq_input.fastq_input1.reverse}" reads_2.fastq
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22 #set $fastqs = ['reads_1.fastq','reads_2.fastq']
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23 #elif str( $fastq_input.fastq_input_selector ) == "single":
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24 ln -s "${fastq_input.fastq_input1}" reads.fastq
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25 #set $fastqs = ['reads.fastq']
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26 #end if
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1
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27 && cp \$OPTITYPE_DIR/config.ini .
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28 && ln -s \$OPTITYPE_DIR/data data
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0
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29 #set $input_fq = ' '.join($fastqs)
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1
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30 && python \$OPTITYPE_DIR/OptiTypePipeline.py
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31 $read_type --input ${' '.join($fastqs)}
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2
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32 #if str($beta) != '':
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33 --beta $beta
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34 #end if
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2
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35 #if str($enumerations) != '':
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36 --enumerate $enumerations
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37 #end if
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1
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38 --outdir $outdir
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39 && cp $outdir/*/*_coverage_plot.pdf $coverage_plot
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40 && cp $outdir/*/*_result.tsv $result
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41 ]]>
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42 </command>
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43 <inputs>
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44 <conditional name="fastq_input">
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45 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
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46 <option value="paired">Paired</option>
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47 <option value="single">Single</option>
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48 <option value="paired_collection">Paired Collection</option>
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49 </param>
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50 <when value="paired">
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51 <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/>
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52 <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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53 </when>
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54 <when value="single">
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55 <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with single reads"/>
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56 </when>
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57 <when value="paired_collection">
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58 <param name="fastq_input1" format="fastqsanger" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
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59 </when>
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60 </conditional>
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61 <param name="read_type" type="select" label="Nucleotide Type" help="">
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62 <option value="--rna">RNA</option>
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63 <option value="--dna">DNA</option>
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64 </param>
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3
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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)"/>
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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)"/>
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67 <param name="outdir" type="hidden" value="output_dir"/>
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68 </inputs>
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69 <outputs>
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70 <data format="pdf" name="coverage_plot" label="${tool.name} on ${on_string} coverage_plot.pdf"/>
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71 <data format="tabular" name="result" label="${tool.name} on ${on_string} result.tsv"/>
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72 </outputs>
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73 <tests>
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74 <test>
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75 </test>
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76 </tests>
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77 <help>
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78 <![CDATA[
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79 **OptiType**
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80 ============
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81
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3
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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.
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83
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84 **INPUTS**
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85
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86 RNA or DNA sequences in fastq format.
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87
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88 **OPTIONS**
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89
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90 --beta <BETA_VALUE> The beta value for for homozygosity detection (see cited paper).
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91 Default: 0.009. Handle with care.
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92 --enumerate <ENUMERATIONS> Number of enumerations.
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93 OptiType will output the optimal solution and the top N-1 suboptimal solutions in the results.
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94 Default: 1
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95
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96
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97 **OUTPUTS**
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98
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99 result.tsv A TAB-separated file of HLA genotyping predictions:
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100
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101 ::
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102
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103 A1 A2 B1 B2 C1 C2 Reads Objective
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104 0 A*31:01 A*68:01 B*40:01 B*51:01 C*15:02 C*03:04 132 128.43599999999998
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105
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106
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107 coverage_plot.pdf Plots of coverage of HLA genotyping predictions
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108
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109 .. _OptiType: https://github.com/FRED-2/OptiType
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110 ]]>
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111 </help>
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112 <citations>
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3
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113 <citation type="doi">10.1093/bioinformatics/btu548</citation>
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114 </citations>
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115 </tool>
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