<tool id="rnaz" name="RNAz" version="0.1.0">
    <description>predicting structurally conserved and thermodynamically stable RNA secondary structures</description>
    <version_command>RNAz --version</version_command>
    <requirements>
        <requirement type="package" version="2.1">rnaz</requirement>
    </requirements>
    <command>
RNAz $input
$forward
$reverse
$both_strands
$dinucleotide
$mononucleotide
$locarnate
$no_shuffle
#if $cutoff_p != -1:
--cutoff=$cutoff_p
#end if
&gt; temp.txt;
grep -v -E "^ |^#|^$" temp.txt &gt; $outfile;
grep -E "^ |^#|^$" temp.txt;
    </command>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
    </stdio>
    <inputs>
        <param format="txt" name="input" type="data" label="Input Alignment File" />
        <param name="forward" type="boolean" checked="false" truevalue="--forward" falsevalue="" label="Score forward strand" help="--forward" />
        <param name="reverse" type="boolean" checked="false" truevalue="--reverse" falsevalue="" label="Score reverse strand" help="--reverse" />
        <param name="both_strands" type="boolean" checked="false" truevalue="-e" falsevalue="" label="Score both strands" help="-e" />
        <param name="cutoff_p" label="Probability cutoff" type="float" value="-1" help="-1 to deactivate"/>
        <param name="dinucleotide" type="boolean" checked="true" truevalue="--dinucleotide" falsevalue="" label="Use dinucleotide shuffled z-scores" help="--dinucleotide" />
        <param name="mononucleotide" type="boolean" checked="true" truevalue="--mononucleotide" falsevalue="" label="Use mononucleotide shuffled z-scores" help="--mononucleotide" />
        <param name="locarnate" type="boolean" checked="false" truevalue="--locarnate" falsevalue="" label="Use decision model for structural alignments" help="--locarnate" />
        <param name="no_shuffle" type="boolean" checked="false" truevalue="--no-shuffle" falsevalue="" label="Never fall back to shuffling" help="--no-shuffle" />
    </inputs>
    <outputs>
        <data name="outfile" format="fasta" />
    </outputs>
    <help>**What it does**
     RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. It can be used in genome wide screens to detect functional RNA structures, as found in noncoding RNAs and cis-acting regulatory elements of mRNAs.


Gruber AR, Findeiss, Washietl S, Hofacker IL, and Stadler PF. 
RNAz 2.0: Improved noncoding rna detection. 
Pac Symp Biocomput, 2010. 15:69–79.
    </help>
</tool>