<tool id="rnaz_randomize_aln" name="RNAz Randomize Aln" version="2.1">
    <requirements>
        <requirement type="package" version="2.1">rnaz</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    rnazRandomizeAln.pl
        --window $window
        --slide $slide
        --level $level
        '$input'
    > '$output'
    ]]></command>
    <inputs>
        <param type="data" name="input" format="text" />
        <param argument="--window" name="window" type="integer" value="120" label="Window size, default 120" />
        <param argument="--slide" name="slide" type="integer" value="120" label="Window step size, default 120" />
        <param argument="--level" name="level" type="integer" value="2" label="Level of coarse graining" />
    </inputs>
    <outputs>
        <data name="output" format="data"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="randomize.aln"/>
            <output name="output" file="notsorandom.aln"/>
        </test>
    </tests>
    <help><![CDATA[
    Usage:
    rnazRandomizeAln.pl [options] [file]
    
    Options:
    -w N, --window=N
    -s N, --slide=N
    Long alignment blocks should be shuffled locally in order to
    maintain local characteristics of the alignment. Therefore
    alignments can be shuffled in windows. You can specify here the
    size of a window and the offset. Defaults are window=120 and
    slide=120, i.e. the alignments are shuffled in non-overlapping
    windows of 120 columns.
    
    -l N, --level=N
    The shuffling algorithm tries to mantain local conservation
    patterns, i.e. it shuffles only columns of the same degree of
    conservation. This becomes limiting if you have many sequences
    in your alignment. Therfore you can choose the level of coarse
    graining with this option.
    
    To decide which columns have the same degree of conservation,
    the mean pairwise identity (MPI) of each column is calculated
    and finally only columns of the same value are shuffled. You can
    adjust the rounding of the MPI and thus the coarse graining
    level with this option. If you have two columns with say 0.52
    and 0.48 MPI you get:
    
    level 0: 1 and 0
    
    level 1: 50 and 50
    
    level 2: 52 and 48
    
    So on level 0 you only have conserved (MPI > 0.5) and
    non-conserved (MPI < 0.5) columns while on level 2 you need
    almost exactly the same MPI to shuffle two columns.
    
    Default value is 2.


    ]]></help>

    <citations>
        <citation type="doi">10.1142/9789814295291_0009</citation>
    </citations>    

</tool>