view clustalomega/rgClustalOmega.xml @ 0:ea6d0e588642 default tip

Migrated tool version 0.2 from old tool shed archive to new tool shed repository

<tool id="clustalomega" name="Clustal Omega" version="0.2">
<description>
multiple sequence alignment program for proteins
</description>
<command interpreter="python">
hide_stderr.py clustalo --force --threads=1 --maxnumseq=300000 --maxseqlen=15000 -o $output -l $outlog -v 
#if ($basicmode.mode=="mode1")
 -i $input
#elif ($basicmode.mode=="mode2")
 --profile1 $profile1 --profile2 $profile2
#elif ($basicmode.mode=="mode3")
 -i $input --profile1 $profile
#elif ($basicmode.mode=="mode4")
 -i $input --hmm-in=$hmm
#end if
#if($advanced.options=="true")
    #if ($advanced.dealign.value=="Yes")
     --dealign
    #end if
    #if ($advanced.mbed.value=="Yes")
     --mbed
    #end if
    #if ($advanced.iteration.iteroptions =="true")
        --iter $advanced.iteration.iters
        #if ($advanced.iteration.mbediter.value=="Yes")
         --mbed-iter
        #end if
        #if ($advanced.iteration.separateiters.separateiteroptions =="true")
         --max-guidetree-iterations=$advanced.iteration.separateiters.gtiters
         --max-hmm-iterations=$advanced.iteration.separateiters.hmmiters
        #end if
    #end if
    #if ($advanced.dotree.value=="Yes")
     --guidetree-out=$outtree
    #end if
    #if ($advanced.domatrix.value=="Yes")
     --distmat-out=$outmatrix
    #end if
#end if

</command>

<inputs>

<conditional name="basicmode">
    <param name="mode" type="select">
    <label>Alignment mode</label>
    <option value="mode1" selected="true">align sequences</option>
    <option value="mode2">align two profiles</option>
    <option value="mode3">align sequences to a profile</option>
    <option value="mode4">align sequences with a HMM background</option>
    </param>

    <when value="mode1">
        <param name="input" format="fasta" type="data">
        <label>Input sequences</label>
        <help>A fasta file containing the proteins to be aligned</help>
        </param>
    </when>

    <when value="mode2">
        <param name="profile1" format="fasta" type="data">
        <label>Profile 1</label>
        <help>A fasta file containing aligned sequences</help>
    </param>

    <param name="profile2" format="fasta" type="data">
        <label>Profile 2 (Fasta File)</label>
        <help>A fasta file containing aligned sequences</help>
        </param>
    </when>

    <when value="mode3">
        <param name="input" format="fasta" type="data">
        <label>Input sequences</label>
        <help>A fasta file containing the proteins to be aligned</help>
        </param>

        <param name="profile" format="fasta" type="data">
        <label>Profile</label>
        <help>A fasta file containing aligned sequences</help>
        </param>
    </when>

    <when value="mode4">
        <param name="input" format="fasta" type="data">
        <label>Input sequences</label>
        <help>A fasta file containing the proteins to be aligned</help>
        </param>
        
        <param name="hmm" format="other" type="data">
        <label>HMM</label>
        <help>A HMM in HMMER2 or HMMER3 format</help>
        </param>
    </when>
</conditional>
    <param name="outname" label="Name for output files" type="text" size="50" value="co_alignment" />
    
    <conditional name="advanced">
      <param name="options" type="select" label="Advanced Options">
        <option value="false" selected="true">Hide advanced options</option>
        <option value="true">Show advanced options</option>
      </param>
      <when value="false">
        <!-- no options -->
      </when>
      <when value="true">

        <param name="dealign" type="select" display="checkboxes" multiple="True">
        <label>Dealign input sequences (if aligned)</label>
        <option value="Yes">Yes</option>
        <help>If given already aligned sequences, by default Clustal Omega use the existing alignment to guide creation of the new alignment, by constructing a HMM from the existing alignment. Check this box to realign aligned sequences from scratch.</help>
        </param>

        <param name="mbed" type="select" display="checkboxes" multiple="True" label="Use mBed">
        <option value="Yes">Yes</option>
            <help>Use embedding to calculate the guide tree more quickly and using less memory. Should be turned on 
            when more than a thousand sequences are used.</help>
        </param>
        
        <conditional name="iteration">
          <param name="iteroptions" type="select" label="Use iteration">
            <option value="false" selected="true">Do not use iteration</option>
            <option value="true">Use iteration</option>
            <help>Redo the alignment multiple times to improve accuracy. Both the HMM and the guide tree
            will be recalculated each time.</help>
          </param>
          <when value="false">
            <!-- no options -->
          </when>
          <when value="true">
            <param name="iters" type="integer" value="1" label="Number of iterations"></param>

            <param name="mbediter" type="select" display="checkboxes" multiple="True" label="Use MBED for iteration">
                <option value="Yes">Yes</option>
            </param>
                <conditional name="separateiters">
                  <param name="separateiteroptions" type="select">
                    <label>Have a different number of guide tree, HMM iterations</label>
                    <option value="false" selected="true">No</option>
                    <option value="true">Yes</option>
                    <help>Normally, if iteration is specified, a new guide tree and HMM will be calculated for each iteration. Use this option to restrict the number of iterations for either.</help>
                  </param>
                  <when value="false">
                    <!-- no options -->
                  </when>
                  <when value="true">
                    <param name="gtiters" type="integer" value="1" label="Guidetree iterations"></param>
                    <param name="hmmiters" type="integer" value="1" label="HMM iterations"></param>
                  
                  </when>
                </conditional>
          </when>
          </conditional>
      </when>
      </conditional>
        <param name="dotree" type="select" display="checkboxes" multiple="True" label="Output guide tree">
            <option value="Yes">Yes</option>
        </param>
        <param name="domatrix" type="select" display="checkboxes" multiple="True" label="Output distance matrix">
            <option value="Yes">Yes</option>
        </param>
</inputs>

<outputs>
    <data format="fasta" name="output" label="${outname}.fasta" />
    <data format="txt" name="outlog" label="${outname}_log.txt" />
    <data format="txt" name="outtree" label="${outname}_guidetree.txt">
        <filter>dotree=="Yes"</filter>
    </data>
    <data format="txt" name="outmatrix" label="${outname}_distances.txt">
        <filter>domatrix=="Yes"</filter>
    </data>
</outputs>

<tests>
    <test>
        <param name="mode" value="mode1" />
        <param name="input" value="clustalo_unaligned_all.fasta" ftype="fasta" />
        <param name="outname" value="test_output" />
        <param name="options" value="false" />
        <output name="output" file="clustalo_test1_out.fasta" ftype="fasta" lines_diff="200" />
    </test>
    <test>
        <param name="mode" value="mode2" />
        <param name="profile1" value="clustalo_aligned1.fasta" />
        <param name="profile2" value="clustalo_aligned2.fasta" />
        <param name="outname" value="test_output" />
        <param name="options" value="false" />
        <output name="output" file="clustalo_profileprofile.fasta"  lines_diff="200" />
    </test>
</tests>

<help>

Clustal-Omega is a general purpose multiple sequence alignment (MSA)
program for proteins. It produces high quality MSAs and is capable of
handling data-sets of hundreds of thousands of sequences in reasonable
time.

In default mode, users give a file of sequences to be aligned and
these are clustered to produce a guide tree and this is used to guide
a "progressive alignment" of the sequences.  There are also facilities
for aligning existing alignments to each other, aligning a sequence to
an alignment and for using a hidden Markov model (HMM) to help guide
an alignment of new sequences that are homologous to the sequences
used to make the HMM.  This latter procedure is referred to as
"external profile alignment" or EPA.

Clustal-Omega uses HMMs for the alignment engine, based on the HHalign
package from Johannes Soeding [1].  Guide trees are optionally made
using mBed [2] which can cluster very large numbers of sequences in
O(N*log(N)) time.  Multiple alignment then proceeds by aligning larger
and larger alignments using HHalign, following the clustering given by
the guide tree.

In its current form Clustal-Omega can only align protein sequences but
not DNA/RNA sequences. It is envisioned that DNA/RNA will become
available in a future version.

A full version of these instructions is available at http://www.clustal.org/

This is a beta version of Clustal Omega. Bugs should be reported to [e-mail]

A standalone version of Clustal Omega for Linux/Windows/Mac is available from http://www.clustal.org/

[1] Johannes Soding (2005) Protein homology detection by HMM-HMM
    comparison. Bioinformatics 21 (7): 951–960.

[2] Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG.  Sequence
    embedding for fast construction of guide trees for multiple
    sequence alignment.  Algorithms Mol Biol. 2010 May 14;5:21.

</help>
</tool>