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<tool id="ctat_metagenomics" name="ctat_metagenomics" version="1.0.0" profile="17.05">

    <description>Centrifuge classifier for metagenomic sequences (RNA-Seq)</description>
    <requirements>
        <requirement type="package" version="1.0.3=py27pl5.22.0_2">centrifuge</requirement>
        <requirement type="package" version="1.0.1">ctat-metagenomics</requirement>
    </requirements>
    <command detect_errors="default">
      <![CDATA[     
      metagenomics
 
      --index "${index.fields.path}" 
      --out_dir "centrifuge"

      #if $format_type.format == "fasta" 
          --format fasta --unpaired_reads $format_type.fasta_file
      #end if

      #if $format_type.format == "fastq"
          --format fastq
          #if $format_type.read_type.type == "single"
              --read_type "single" --unpaired_reads $format_type.read_type.left_fq_single
          #end if

          #if $format_type.read_type.type == "paired"
               --read_type "paired" --left_fq $format_type.read_type.left_fq --right_fq $format_type.read_type.right_fq  
          #end if 
      #end if

      --threads 4 
      ]]>
    </command>
    <stdio>
        <exit_code range="1:"  level="fatal"   description="Error running centrifuge" />
    </stdio>

    <inputs>

        <conditional name="format_type">
            <param name= "format" type="select" label="Choose input format" help="Choose fasta for Trinity assembled reads">
                <option value="fasta" selected="true">FASTA</option>
                <option value="fastq" selected="false">FASTQ</option>
            </param>
            <when value="fasta">
                <param name="fasta_file" type="data" format="fasta" label="Fasta file:" help="Trinity assembled reads in fasta format"/>
            </when>
            <when value="fastq">
                <conditional name="read_type">
                    <param name= "type" type="select" label="Choose read type" help="Choose read type">
                        <option value="single" selected="true">SINGLE END DATA</option>
                        <option value="paired" selected="false">PAIRED END DATA</option>
                    </param>
                    <when value="single">
                        <param name="left_fq_single" type="data" format="fastq" label="Left_fq:" help="Left fastq"/>
                    </when>
                    <when value="paired">
                        <param name="left_fq" type="data" format="fastq" label="Left_fq:" help="Left fastq"/>
                        <param name="right_fq" type="data" format="fastq" label="Right_fq:" help="Right fastq"/>
                    </when>
                </conditional>
            </when>
        </conditional>

        <param name="index" type="select" label="Choose reference genome index :" help="Select genome index">
            <options from_data_table="ctat_centrifuge_indexes" />
        </param>
      
    </inputs>

    <outputs>
        <data format="txt" name="classification_results" label="Centrifuge classification output" from_work_dir="centrifuge/classification.results.txt"/>
        <data format="txt" name="classification_report" label="Centrifuge summary output" from_work_dir="centrifuge/classification.report.txt"/>
        <data format="txt" name="kraken_style_report" label="Kraken-style report" from_work_dir="centrifuge/kraken_style_report.txt"/>
    </outputs>

    <tests>
        <test>
            <!-- The following test uses one file that is unpaired reads.
            -->
            <param name="format" value="fastq" />
            <param name="type" value="single" />
            <param name="left_fq_single" value="centrifuge/SRR2219890_1.adj.fastq" />
            <param name="index" value="/N/dc2/projects/galaxyshared/trinity/dev/Trinity_CTAT/metagenomics/phv" />
            <output name="classification_results" >
                <assert_contents>
                    <has_line_matching expression=".+" />
                    <has_line line="readID&#009;seqID&#009;taxID&#009;score&#009;2ndBestScore&#009;hitLength&#009;queryLength&#009;numMatches" />
                </assert_contents>
            </output>
            <output name="classification_report" file="centrifuge/SRR2219890_1.classification.report.txt" />
            <output name="kraken_style_report" file="centrifuge/SRR2219890_1.kraken_style_report.txt" />
        </test>
    </tests>

    <help>
.. class:: infomark
 
ctat_metagenomics is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). CTAT's metagenomics is a classifier for metagenomic sequences (RNA-Seq) for foreign transcript detection. It leverages Centrifuge, a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species, and Kraken. As well, we are leveraging RNA-Seq reads and Trinity-reconstructed transcripts. Our efforts here are being carried out in collaboration with the group of Steven Salzberg at JHU.

For more information:

https://ccb.jhu.edu/software/centrifuge/manual.shtml#what-is-centrifuge

    </help>
<citations>
      <citation type="doi">10.1101/gr.210641.116</citation>
</citations>
</tool>