--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/selectsequencesfrommsa.xml	Sat Mar 11 16:59:55 2017 -0500
@@ -0,0 +1,62 @@
+<tool id="selectsequencesfrommsa" name="Select Sequences" version="1.0.2">
+  <description>
+    Tool to select representative sequences from a multiple sequence alignment.
+  </description>
+  <requirements>
+    <requirement type="package" version="1.0.2">selectsequencesfrommsa</requirement>
+  </requirements>
+  <command detect_errors="aggressive"><![CDATA[
+    SelectSequencesFromMSA
+      -c '$input_clustal'
+      $x
+      -o `pwd`
+      -n $n
+      -i $i
+      -m $m
+      > warnings
+    ]]>
+  </command>
+  <inputs>
+    <param name="input_clustal" type="data" format="clustal" label="Input clustal alignment"/>
+    <param argument="-n" type="integer" value="6" min="1" label="Number of sequences in the output alignment." help=""/>
+    <param argument="-i" type="float" value="80" min="0.1" label="Optimize for this percentage of mean pairwise identity" help=""/>
+    <param argument="-m" type="float" value="95" min="0.1" label="Sequences with a higher percentage of pairwise identity will be removed." help=""/>
+    <param argument="-x" truevalue="-x" falsevalue="" checked="True" type="boolean" label="The first sequence (=reference sequence) is always present in the output alignment." help=""/>
+  </inputs>
+  <outputs>
+    <data format="clustal" name="clustal" from_work_dir="result.selected" label="Clustal alignment of selected sequences"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_clustal" value="result.clustal"/>
+      <output name="result.selected" file="result.selected"/>
+    </test>
+  </tests>
+  <help>
+    
+<![CDATA[
+             
+**What it does**
+
+Tool to select representative sequences from a multiple sequence alignment in clustal format.
+Useful before running RNAz, RNAcode, RNAalifold on alignments with many entries.
+
+**Input**
+Multiple sequence alignment in clustal format
+
+**Options**
+-n Number of sequences in the output alignment. (Default: 6)
+-i Optimize for this percentage of mean pairwise identity (Default: 80)
+-m Sequences with a higher percentage of pairwise identity will be removed (Default: 95)
+-x The first sequence (=reference sequence) is always present in the output alignment per default. Default: True
+
+**Output**
+Clustal alignment with selected sequences
+
+]]>
+
+  </help>
+  <citations>
+    <citation type="doi">10.1093/nar/gkw558</citation>
+  </citations>
+</tool>