view optitype.xml @ 3:4f78281c42ff draft

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<tool id="optitype" name="OptiType" version="1.0.0">
  <description>HLA genotyping predictions from NGS data</description>
  <requirements>
    <requirement type="package" version="1.8.12">hdf5</requirement>
    <requirement type="package" version="3.4.0">razers3</requirement>
    <requirement type="package" version="1.0">optitype</requirement>
    <requirement type="package" version="2.9.5">cbc</requirement>
  </requirements>
 <stdio>
     <exit_code range="1:"  level="fatal" description="Error Running optitype" />
 </stdio>
  <command>
<![CDATA[
#set $fastqs = []
#if str( $fastq_input.fastq_input_selector ) == "paired":
  ln -s "${fastq_input.fastq_input1}" reads_1.fastq
  && ln -s "${fastq_input.fastq_input2}" reads_2.fastq
  #set $fastqs = ['reads_1.fastq','reads_2.fastq']
#elif str( $fastq_input.fastq_input_selector ) == "paired_collection":
  ln -s "${fastq_input.fastq_input1.forward}" reads_1.fastq
  && ln -s "${fastq_input.fastq_input1.reverse}" reads_2.fastq
  #set $fastqs = ['reads_1.fastq','reads_2.fastq']
#elif str( $fastq_input.fastq_input_selector ) == "single":
  ln -s "${fastq_input.fastq_input1}" reads.fastq
  #set $fastqs = ['reads.fastq']
#end if
&& cp \$OPTITYPE_DIR/config.ini .
&& ln -s \$OPTITYPE_DIR/data data
#set $input_fq = ' '.join($fastqs)
&& python  \$OPTITYPE_DIR/OptiTypePipeline.py 
$read_type --input  ${' '.join($fastqs)}
#if str($beta) != '': 
 --beta $beta
#end if
#if str($enumerations) != '': 
 --enumerate $enumerations
#end if
--outdir $outdir
&& cp $outdir/*/*_coverage_plot.pdf $coverage_plot
&& cp $outdir/*/*_result.tsv $result
]]>
  </command>
  <inputs>
    <conditional name="fastq_input">
      <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
        <option value="paired">Paired</option>
        <option value="single">Single</option>
        <option value="paired_collection">Paired Collection</option>
      </param>
      <when value="paired">
        <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/>
        <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/>
      </when>
      <when value="single">
        <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with single reads"/>
      </when>
      <when value="paired_collection">
        <param name="fastq_input1" format="fastqsanger" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
      </when>
    </conditional>
    <param name="read_type" type="select" label="Nucleotide Type" help="">
      <option value="--rna">RNA</option>
      <option value="--dna">DNA</option>
    </param>
    <param name="beta" type="float" value="" min="0.0" max="0.1" optional="true" label="homozygosity beta" help="The beta value for for homozygosity detection (Leave blank for default: 0.009)"/>
    <param name="enumerations" type="integer" value="" min="1" max="5" optional="true" label="Enumerations" help="The number of enumerations (Leave blank for default: 1)"/>
    <param name="outdir" type="hidden" value="output_dir"/>
  </inputs>
  <outputs>
    <data format="pdf" name="coverage_plot" label="${tool.name} on ${on_string} coverage_plot.pdf"/>
    <data format="tabular" name="result" label="${tool.name} on ${on_string} result.tsv"/>
  </outputs>
  <tests>
    <test>
    </test>
  </tests>
  <help>
<![CDATA[
**OptiType**
============

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.

**INPUTS** 

   RNA or DNA sequences in fastq format.

**OPTIONS**

  --beta <BETA_VALUE>           The beta value for for homozygosity detection (see cited paper). 
                                Default: 0.009. Handle with care.
  --enumerate <ENUMERATIONS>    Number of enumerations. 
                                OptiType will output the optimal solution and the top N-1 suboptimal solutions in the results. 
                                Default: 1


**OUTPUTS**

  result.tsv   A TAB-separated file of HLA genotyping predictions:

  ::

		A1	A2	B1	B2	C1	C2	Reads	Objective
	0	A*31:01	A*68:01	B*40:01	B*51:01	C*15:02	C*03:04	132	128.43599999999998


  coverage_plot.pdf  Plots of coverage of HLA genotyping predictions

.. _OptiType: https://github.com/FRED-2/OptiType
]]>
  </help>
  <citations>
    <citation type="doi">10.1093/bioinformatics/btu548</citation>
  </citations>
</tool>