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comparison 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
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children 54c9c71dabe8
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-1:000000000000 0:3902a76bf089
1 <tool id="optitype" name="OptiType" version="1.3.2">
2 <description>HLA genotyping predictions from NGS data</description>
3 <requirements>
4 <requirement type="package" version="1.3.2">optitype</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" level="fatal" description="Error Running optitype" />
8 </stdio>
9 <command>
10 <![CDATA[
11 #set $fastqs = []
12 #if str( $fastq_input.fastq_input_selector ) == "paired":
13 ln -s "${fastq_input.fastq_input1}" reads_1.fastq
14 && ln -s "${fastq_input.fastq_input2}" reads_2.fastq
15 #set $fastqs = ['reads_1.fastq','reads_2.fastq']
16 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection":
17 ln -s "${fastq_input.fastq_input1.forward}" reads_1.fastq
18 && ln -s "${fastq_input.fastq_input1.reverse}" reads_2.fastq
19 #set $fastqs = ['reads_1.fastq','reads_2.fastq']
20 #elif str( $fastq_input.fastq_input_selector ) == "single":
21 ln -s "${fastq_input.fastq_input1}" reads.fastq
22 #set $fastqs = ['reads.fastq']
23 #end if
24 && cp \$OPTITYPE_DIR/config.ini .
25 && ln -s \$OPTITYPE_DIR/data data
26 #set $input_fq = ' '.join($fastqs)
27 && python \$OPTITYPE_DIR/OptiTypePipeline.py
28 $read_type --input ${' '.join($fastqs)}
29 #if str($beta) != '':
30 --beta $beta
31 #end if
32 #if str($enumerations) != '':
33 --enumerate $enumerations
34 #end if
35 --outdir $outdir
36 && cp $outdir/*/*_coverage_plot.pdf $coverage_plot
37 && cp $outdir/*/*_result.tsv $result
38 ]]>
39 </command>
40 <inputs>
41 <conditional name="fastq_input">
42 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
43 <option value="paired">Paired</option>
44 <option value="single">Single</option>
45 <option value="paired_collection">Paired Collection</option>
46 </param>
47 <when value="paired">
48 <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/>
49 <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/>
50 </when>
51 <when value="single">
52 <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with single reads"/>
53 </when>
54 <when value="paired_collection">
55 <param name="fastq_input1" format="fastqsanger" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
56 </when>
57 </conditional>
58 <param name="read_type" type="select" label="Nucleotide Type" help="">
59 <option value="--rna">RNA</option>
60 <option value="--dna">DNA</option>
61 </param>
62 <param name="beta" type="float" value="" min="0.0" max="0.1" optional="true" label="homozygosity beta" help="The beta value for for homozygosity detection (Leave blank for default: 0.009)"/>
63 <param name="enumerations" type="integer" value="" min="1" max="5" optional="true" label="Enumerations" help="The number of enumerations (Leave blank for default: 1)"/>
64 <param name="outdir" type="hidden" value="output_dir"/>
65 </inputs>
66 <outputs>
67 <data format="pdf" name="coverage_plot" label="${tool.name} on ${on_string} coverage_plot.pdf"/>
68 <data format="tabular" name="result" label="${tool.name} on ${on_string} result.tsv"/>
69 </outputs>
70 <tests>
71 <test>
72 </test>
73 </tests>
74 <help>
75 <![CDATA[
76 **OptiType**
77 ============
78
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.
80
81 **INPUTS**
82
83 RNA or DNA sequences in fastq format.
84
85 **OPTIONS**
86
87 --beta <BETA_VALUE> The beta value for for homozygosity detection (see cited paper).
88 Default: 0.009. Handle with care.
89 --enumerate <ENUMERATIONS> Number of enumerations.
90 OptiType will output the optimal solution and the top N-1 suboptimal solutions in the results.
91 Default: 1
92
93
94 **OUTPUTS**
95
96 result.tsv A TAB-separated file of HLA genotyping predictions:
97
98 ::
99
100 A1 A2 B1 B2 C1 C2 Reads Objective
101 0 A*31:01 A*68:01 B*40:01 B*51:01 C*15:02 C*03:04 132 128.43599999999998
102
103
104 coverage_plot.pdf Plots of coverage of HLA genotyping predictions
105
106 .. _OptiType: https://github.com/FRED-2/OptiType
107 ]]>
108 </help>
109 <citations>
110 <citation type="doi">10.1093/bioinformatics/btu548</citation>
111 </citations>
112 </tool>