<tool id="clustalw" name="ClustalW" version="0.1">
   <description>multiple sequence alignment program for DNA or proteins</description>
   <command interpreter="python"> 
    rgClustalw.py -i "$input" -o "$output" -s "$out_order" -l "$outlog" -t "$outname" -d "$dnarna"
    #if   ($range.mode=="part")
-b "$range.seq_range_start" -e "$range.seq_range_end"
    #end if
    #if ($outcontrol.outform=="clustal")
-f "CLUSTAL"
    #if ($outcontrol.out_seqnos=="ON")
-q "ON"
    #end if
    #end if
    #if ($outcontrol.outform=="phylip")
-f "PHYLIP"
    #end if
    #if ($outcontrol.outform=="fasta")
-f "FASTA"
    #end if
   </command>
  <inputs>
   <page>
    <param format="fasta" name="input" type="data" label="Fasta File" />
    <param name="outname" label="Name for output files to make it easy to remember what you did" type="text" size="50" value="Clustal_run" />
    <param name="dnarna" type="select" label="Data Type">
      <option value="DNA" selected="True">DNA nucleotide sequences</option>
      <option value="PROTEIN">Protein sequences</option>
    </param>
    <conditional name="outcontrol">
      <param name="outform" type="select" label="Output alignment format">
        <option value="clustal" selected="True">Native Clustal output format</option>
        <option value="phylip">Phylip format</option>
        <option value="fasta">Fasta format</option>
      </param>
      <when value="fasta" />
      <when value="phylip" />
      <when value="clustal">
       <param name="out_seqnos" type="select" label="Show residue numbers in clustal format output">
         <option value="ON">yes</option>
         <option value="OFF" selected="true">no</option>
       </param>
      </when>
    </conditional>
    <param name="out_order" type="select" label="Output Order">
      <option value="ALIGNED">aligned</option>
      <option value="INPUT">same order as input file</option>
    </param>

    <conditional name="range">
        <param name="mode" type="select" label="Output complete alignment (or specify part to output)">
          <option value="complete">complete alignment</option>
          <option value="part">only part of the alignment</option>
        </param>
        <when value="complete">
        </when>
        <when value="part">    
           <param name="seq_range_start" size="5" type="integer" value="1" label="start point" help="sequence range to write">
           </param>
           <param name="seq_range_end" size="5" type="integer" value="99999" label="end point" >
           </param> 
        </when>
    </conditional>
   </page>
  </inputs>
  <outputs>
    <data format="clustal" name="output"  label="${outname}_output.${outcontrol.outform}">
       <change_format>
           <when input="outcontrol.outform" value="phylip" format="phylip" />
           <when input="outcontrol.outform" value="fasta" format="fasta" />
       </change_format>
    </data>
    <data format="txt" name="outlog"  label="${outname}_clustal_log.txt"/>
  </outputs>
  <tests>
     <test>
        <param name="input" value="rgClustal_testin.fasta" />
      <param name = "outname" value="" />
      <param name = "outform" value="fasta" />
      <param name = "dnarna" value="DNA" />
      <param name = "mode" value="complete" />
      <param name = "out_order" value="ALIGNED" />
      <output name="output" file="rgClustal_testout.fasta" ftype="fasta" />
      <output name="outlog" file="rgClustal_testout.log" ftype="txt" lines_diff="5" />
     </test>
  </tests>
  <help>

**Note**

This tool allows you to run a multiple sequence alignment with ClustalW2 (see Clustsrc_) using the default options.
 
For a tutorial introduction, see ClustalW2_

You can align DNA or protein sequences in the input file which should be multiple sequences to be aligned in a fasta file

A log will be output to your history showing the output Clustal would normally write to standard output.

The alignments will appear as a clustal format file or optionally, as phylip or fasta format files in your history. If you choose fasta as 
the output format, you can create a 'Logo' image using the Sequence Logo tool.

If Clustal format is chosen, you have the option of adding basepair counts to the output

A subsequence of the alignment can be output by setting the Output complete parameter to "Partial" and defining the offset and end of the subsequence to be output 

----

**Attribution**

Clustal attribution and associated documentation are available at Clustsrc_

The first iteration of this Galaxy wrapper was written by Hans-Rudolf Hotz - see Clustfirst_

It was modified by Ross Lazarus for the rgenetics project - tests and some additional parameters were added

This wrapper is released licensed under the LGPL_

.. _ClustalW2: http://www.ebi.ac.uk/2can/tutorials/protein/clustalw.html  

.. _Clustsrc: http://www.clustal.org

.. _Clustfirst: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html

.. _LGPL: http://www.gnu.org/copyleft/lesser.html

  </help>

</tool>