rRNA_prediction.xml

<tool id="meta_rna" name="rRNA" version="0.1">
    <description>Identification of ribosomal RNA genes in metagenomic fragments</description>
    <requirements>
        <requirement type="binary">hmmsearch3.0</requirement>
    </requirements>
    <command interpreter='python'>
<![CDATA[
        rna_hmm3.py
            --cpu "\${GALAXY_SLOTS:-4}"
            -i $input
            -L /home/galaxy/lib/meta_rna/HMM3
            -k $kingdom
            -e $evalue

            #if(str($isMaskFile)=='yes')
                --mask $MaskSequenceFile
            #end if
            #if(str($isSequenceFile)=='yes')
                --seq $SequenceFile
            #end if

            --gff $GFFFile

            #please set export PATH=/path_to_hmm3_search
            #and adjust the -L parameter

]]>
    </command>
    <inputs>
        <param name="input" type="data" format="fasta" label="Genome Sequence"/>
        <param name="evalue" type="text" value="0.01" label="E-value" help="e-value cut-off for hmmsearch, default 0.01"/>

        <param name="kingdom" type="select" display="checkboxes" multiple="true" label="Kingdom" help="If more than one is used, the program will select best kingdom for the sequence according to evalue">
            <option value="arc" selected="True">Archaeal</option>
            <option value="bac" selected="True">Bacterial</option>
            <option value="euk" selected="True">Eukaryotic</option>
        </param>

        <param name="isMaskFile" type="select" label="Mask fasta sequence as additional output?">
              <option value="yes">yes</option>
              <option value="no" selected="True">no</option>
        </param>
        <param name="isSequenceFile" type="select" label="Fasta sequence as additional output?">
              <option value="yes">yes</option>
              <option value="no" selected="True">no</option>
        </param>

    </inputs>
    <outputs>
        <data format="gff" name="GFFFile" label="rRNA coordinate file"/>
        <data format="fasta" name="MaskSequenceFile" label="rRNA sequences">
            <filter>isMaskFile == "yes"</filter>
        </data>
        <data format="fasta" name="SequenceFile" label="rRNA sequences">
            <filter>isSequenceFile == "yes"</filter>
        </data>
    </outputs>
    <help>
<![CDATA[

**What it does**

Identification of ribosomal RNA genes in metagenomic fragments.


**Input**

Nucleotide sequence in FASTA format.


**Example**

Suppose you have the following DNA formatted sequences::

	>seq1
	CACGTGGAATCCCGTTTGAAGATAGGAGGACCATCTCCTAAGGCTAAATACTACTTGGTG
	ACCGATAGTGAACCAGTACAGTGATGGAAAGGTGAAAAGAACCCCGGGAGGGGAGTGAAA
	GAGAACCTGAAACTGTGTGCTTACAATTAGTCAGAGCCCGTTAATGGGTGATGGCATGCC
	TTTTGTAGAATGAACCGGCGAGTTATGTTACATAGCAAGGTTAAGGATGAAGGTCCGGAG
	CCGAAGCGAAAGCGAGTCTGAATAGGGCGCTTAAGTTGTGTGATGTAGACCCGAAACTGG
	GTGATCTAGCCATGAGCAGGTTGAAGTAAGGGTAGTACCTTATGGAGGACCGAACCGCCG
	CCTGTTGAAAAAGGCTCGGATGACTTGTGGCTAGGGGAGA


Running this tool will produce this::
	##seq_name	method	feature	start	end	evalue	strand	gene
	seq1	rna_hmm3	rRNA	1	400	1.3e-120	+	Bacterial:23S_rRNA

]]>

    </help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btp161</citation>
    </citations>
</tool>