view seq2HLA.xml @ 1:155b796033b6 draft default tip

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<tool id="seqhla" name="seq2HLA" version="1.0.0">
    <description>HLA typing from RNA-Seq sequence read</description>
    <command interpreter="python">
      seq2HLA.py
      -t $threads
      -z $compressed
      -1 $readFile1
      -2 $readFile2
      -r $runName
      -l $readLength
      -3 $trim
      -o $out1
      -p $out2
      -g $logfile
    </command>
    <inputs>
      <param name="compressed" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Select if your input files are compressed gzipped fastq files" help="Leave default (not checked) if you are unsure"/>
      <param format="fastq,fastqsanger" name="readFile1" type="data" label="Forward FASTQ File" help="FASTQ File with forward reads" />
      <param format="fastq,fastqsanger" name="readFile2" type="data" label="Reverse FASTQ File" help="FASTQ File with reverse reads" />
      <param name="runName" type="text" value="Run1" label="Run Name" help="Name of the Run" />
      <param name="readLength" type="integer" value="50" label="Read Length" help="Length of the input reads" />
      <param name="trim" type="integer" value="0" label="Trim x bases from the low quality 3' end" help="Trim x bases from the low quality 3' end. Default: 0" />
      <param name="threads" type="integer" value="4" label="Number of threads to use for Bowtie" help="Choose a plausible amount of threads to use for Bowtie in this tool" />
    </inputs>
    <outputs>
      <data format="txt" name="out1" label="${tool.name} on ${on_string}: Output 1" />
      <data format="txt" name="out2" label="${tool.name} on ${on_string}: Output 2" />
      <data format="txt" name="logfile" label="${tool.name} on ${on_string}: Log" />
    </outputs>
    <tests>
      <test>
	<param name="compressed" value="True"/>
	<param name="readFile1" ftype="fastq" value="input1.fq"/>
	<param name="readFile2" ftype="fastq" value="input2.fq"/>
	<param name="runName" value="Run1"/>
	<param name="readLength" value="37"/>
	<param name="trim" value="0"/>
	<param name="threads" value="4"/>
	<output name="out1" file="output1.txt"/>
	<output name="out2" file="output2.txt"/>
	<output name="logfile" file="log.txt"/>
      </test>
    </tests>
<help>
.. class:: infomark

**What it does**

We developed an in-silico method "seq2HLA", written in python and R, which takes standard paired end RNA-Seq sequence reads in fastq format
as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes, a p-value for each call, and the expression of each class.


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.. class:: infomark

**Dependencies**

- bowtie
- R

**Input**

Input files in FASTQ format

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.. class:: infomark

**Output**

Output file(s) in TXT format

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.. class:: infomark

**Authors**

Sebastian Boegel

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.. image:: http://tron-mainz.de/wp-content/themes/tron/images/page_logo.png

</help>
</tool>