view tools/rgenetics/rgClustalw.xml @ 1:cdcb0ce84a1b

author xuebing
date Fri, 09 Mar 2012 19:45:15 -0500
parents 9071e359b9a3
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<tool id="clustalw" name="ClustalW" version="0.1">
   <description>multiple sequence alignment program for DNA or proteins</description>
   <command interpreter="python"> -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")
    #if ($outcontrol.out_seqnos=="ON")
-q "ON"
    #end if
    #end if
    #if ($outcontrol.outform=="phylip")
    #end if
    #if ($outcontrol.outform=="fasta")
-f "FASTA"
    #end if
    <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>
    <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>
      <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 name="out_order" type="select" label="Output Order">
      <option value="ALIGNED">aligned</option>
      <option value="INPUT">same order as input file</option>

    <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>
        <when value="complete">
        <when value="part">    
           <param name="seq_range_start" size="5" type="integer" value="1" label="start point" help="sequence range to write">
           <param name="seq_range_end" size="5" type="integer" value="99999" label="end point" >
    <data format="clustal" name="output"  label="${outname}_output.${outcontrol.outform}">
           <when input="outcontrol.outform" value="phylip" format="phylip" />
           <when input="outcontrol.outform" value="fasta" format="fasta" />
    <data format="txt" name="outlog"  label="${outname}_clustal_log.txt"/>
        <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" />


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 



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:  

.. _Clustsrc:

.. _Clustfirst:

.. _LGPL: