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annotate optitype.xml @ 0:3902a76bf089 draft

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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/optitype commit 92a9a2f36072d19783d111ae15843c47a7a85c87"
author jjohnson
date Thu, 12 Mar 2020 11:32:13 -0400
parents
children 54c9c71dabe8
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3902a76bf089 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/optitype commit 92a9a2f36072d19783d111ae15843c47a7a85c87"
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1 <tool id="optitype" name="OptiType" version="1.3.2">
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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="1.3.2">optitype</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" description="Error Running optitype" />
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8 </stdio>
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9 <command>
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10 <![CDATA[
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11 #set $fastqs = []
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12 #if str( $fastq_input.fastq_input_selector ) == "paired":
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13 ln -s "${fastq_input.fastq_input1}" reads_1.fastq
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14 && ln -s "${fastq_input.fastq_input2}" reads_2.fastq
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15 #set $fastqs = ['reads_1.fastq','reads_2.fastq']
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16 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection":
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17 ln -s "${fastq_input.fastq_input1.forward}" reads_1.fastq
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18 && ln -s "${fastq_input.fastq_input1.reverse}" reads_2.fastq
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19 #set $fastqs = ['reads_1.fastq','reads_2.fastq']
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20 #elif str( $fastq_input.fastq_input_selector ) == "single":
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21 ln -s "${fastq_input.fastq_input1}" reads.fastq
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22 #set $fastqs = ['reads.fastq']
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23 #end if
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24 && cp \$OPTITYPE_DIR/config.ini .
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25 && ln -s \$OPTITYPE_DIR/data data
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26 #set $input_fq = ' '.join($fastqs)
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27 && python \$OPTITYPE_DIR/OptiTypePipeline.py
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28 $read_type --input ${' '.join($fastqs)}
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29 #if str($beta) != '':
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30 --beta $beta
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31 #end if
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32 #if str($enumerations) != '':
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33 --enumerate $enumerations
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34 #end if
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35 --outdir $outdir
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36 && cp $outdir/*/*_coverage_plot.pdf $coverage_plot
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37 && cp $outdir/*/*_result.tsv $result
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38 ]]>
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39 </command>
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40 <inputs>
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41 <conditional name="fastq_input">
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42 <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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43 <option value="paired">Paired</option>
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44 <option value="single">Single</option>
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45 <option value="paired_collection">Paired Collection</option>
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46 </param>
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47 <when value="paired">
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48 <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/>
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49 <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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50 </when>
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51 <when value="single">
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52 <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with single reads"/>
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53 </when>
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54 <when value="paired_collection">
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55 <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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56 </when>
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57 </conditional>
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58 <param name="read_type" type="select" label="Nucleotide Type" help="">
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59 <option value="--rna">RNA</option>
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60 <option value="--dna">DNA</option>
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61 </param>
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62 <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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63 <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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64 <param name="outdir" type="hidden" value="output_dir"/>
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65 </inputs>
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66 <outputs>
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67 <data format="pdf" name="coverage_plot" label="${tool.name} on ${on_string} coverage_plot.pdf"/>
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68 <data format="tabular" name="result" label="${tool.name} on ${on_string} result.tsv"/>
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69 </outputs>
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70 <tests>
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71 <test>
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72 </test>
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73 </tests>
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74 <help>
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75 <![CDATA[
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76 **OptiType**
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77 ============
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78
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79 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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80
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81 **INPUTS**
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82
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83 RNA or DNA sequences in fastq format.
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84
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85 **OPTIONS**
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86
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87 --beta <BETA_VALUE> The beta value for for homozygosity detection (see cited paper).
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88 Default: 0.009. Handle with care.
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89 --enumerate <ENUMERATIONS> Number of enumerations.
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90 OptiType will output the optimal solution and the top N-1 suboptimal solutions in the results.
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91 Default: 1
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92
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93
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94 **OUTPUTS**
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95
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96 result.tsv A TAB-separated file of HLA genotyping predictions:
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97
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98 ::
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99
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100 A1 A2 B1 B2 C1 C2 Reads Objective
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101 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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102
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103
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104 coverage_plot.pdf Plots of coverage of HLA genotyping predictions
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105
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106 .. _OptiType: https://github.com/FRED-2/OptiType
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107 ]]>
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108 </help>
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109 <citations>
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110 <citation type="doi">10.1093/bioinformatics/btu548</citation>
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111 </citations>
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112 </tool>