--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnazRandomizeAln.xml	Wed Jan 30 04:12:32 2019 -0500
@@ -0,0 +1,75 @@
+<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>