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comparison optitype.xml @ 0:887bc9c92c05 draft

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author jjohnson
date Thu, 27 Aug 2015 17:07:26 -0400
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1 <tool id="optitype" name="OptiType" version="1.0.0">
2 <description>HLA genotyping predictions from NGS data</description>
3 <requirements>
4 <requirement type="package" version="1.8.12">hdf5</requirement>
5 <requirement type="package" version="3.4.0">razers3</requirement>
6 <requirement type="package" version="1.0">optitype</requirement>
7 <requirement type="package" version="2.9.5">cbc</requirement>
8 </requirements>
9 <stdio>
10 <exit_code range="1:" level="fatal" description="Error Running optitype" />
11 </stdio>
12 <command>
13 <![CDATA[
14 #set $fastqs = []
15 #if str( $fastq_input.fastq_input_selector ) == "paired":
16 ln -s "${fastq_input.fastq_input1}" reads_1.fastq
17 && ln -s "${fastq_input.fastq_input2}" reads_2.fastq
18 #set $fastqs = ['reads_1.fastq','reads_2.fastq']
19 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection":
20 ln -s "${fastq_input.fastq_input1.forward}" reads_1.fastq
21 && ln -s "${fastq_input.fastq_input1.reverse}" reads_2.fastq
22 #set $fastqs = ['reads_1.fastq','reads_2.fastq']
23 #elif str( $fastq_input.fastq_input_selector ) == "single":
24 ln -s "${fastq_input.fastq_input1}" reads.fastq
25 #set $fastqs = ['reads.fastq']
26 #end if
27 #set $input_fq = ' '.join($fastqs)
28 && python OptiTypePipeline.py
29 $read_type --input ${' '.join($fastqs)}
30 #if $beta != None:
31 --beta $beta
32 #end if
33 #if $enumerate != None:
34 --enumerate $enumerations
35 #end if
36 --output $outdir
37 && cp $outdir/*/*_coverage_plot.pdf $coverage_plot
38 && cp $outdir/*/*_result.tsv $result
39 ]]>
40 </command>
41 <inputs>
42 <conditional name="fastq_input">
43 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
44 <option value="paired">Paired</option>
45 <option value="single">Single</option>
46 <option value="paired_collection">Paired Collection</option>
47 </param>
48 <when value="paired">
49 <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/>
50 <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/>
51 </when>
52 <when value="single">
53 <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with single reads"/>
54 </when>
55 <when value="paired_collection">
56 <param name="fastq_input1" format="fastqsanger" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
57 </when>
58 </conditional>
59 <param name="read_type" type="select" label="Nucleotide Type" help="">
60 <option value="--rna">RNA</option>
61 <option value="--dna">DNA</option>
62 </param>
63 <param name="beta" type="float" value="" min="0.0" max="0.1" optional="true" label="homozygosity beta" help="The beta value for for homozygosity detection"/>
64 <param name="enumerations" type="integer" value="" min="1" max="5" optional="true" label="Enunerations" help="The number of enumerations"/>
65 <param name="outdir" type="hidden" value="output_dir"/>
66 </inputs>
67 <outputs>
68 <data format="pdf" name="coverage_plot" label="${tool.name} on ${on_string} coverage_plot.pdf"/>
69 <data format="tabular" name="result" label="${tool.name} on ${on_string} result.tsv"/>
70 </outputs>
71 <tests>
72 <test>
73 </test>
74 </tests>
75 <help>
76 <![CDATA[
77 **OptiType**
78 ============
79
80 ]]>
81 </help>
82 <citations>
83 <citation type="doi">10.1093/bioinformatics/btu548. Epub 2014 Aug 20.</citation>
84 </citations>
85 </tool>