<tool id="t_coffee" name="T-Coffee" version="11.0.8">
    <description>multiple sequence alignment</description>
    <requirements>
        <requirement type="package" version="11.0.8">t_coffee</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>
    <version_command>
        t_coffee -version | grep Version
    </version_command>
    <command>
<![CDATA[
        #if str($input_type.filter_fasta) == 'yes'
            #set $input = '-infile=stdin'
            python '$__tool_directory__/filter_by_fasta_ids.py' '$input_type.identifiers' '$input_type.fasta_input' |
        #end if

        #set $method_opt = ''
        #if $method01
            #set $method_opt += str($method01) + ','
        #end if
        #if $method02
            #set $method_opt += str($method02) + ','
        #end if
        #if $method03
            #set $method_opt += str($method03) + ','
        #end if
        #if $method_opt
            #set $method_opt = '-method ' + $method_opt[:-1]
        #end if

        #set $output_opt = ''
        #if $outputs
            #set $outputs_arr = str($outputs).split(',')
            #for $o in $outputs_arr
                #if $o not in ['cigar', 'dnd']
                    #set $output_opt += $o + ','
                #end if
            #end for
            #if 'cigar' in $outputs_arr and 'fasta_aln' not in $outputs_arr
                #set $output_opt += 'fasta_aln,'
            #end if
        #else
            #set $outputs_arr = []
        #end if
        #if $output_opt
            #set $output_opt = '-output ' + $output_opt[:-1]
        #end if

        t_coffee '$input' $method_opt $output_opt -n_core \${GALAXY_SLOTS:-1} -run_name t_coffee_out -quiet

        #if 'cigar' in $outputs_arr
            && python '$__tool_directory__/t_coffee_to_cigar.py' t_coffee_out.fasta_aln > '$cigar'
        #end if
]]>
    </command>
    <inputs>
        <conditional name="input_type">
            <param name="filter_fasta" type="select" label="Filter FASTA input?">
                <option value="no">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="yes">
                <param name="fasta_input" type="data" format="fasta" label="FASTA sequences" />
                <param name="identifiers" type="data" format="txt" label="List of FASTA sequence IDs" />
            </when>
            <when value="no">
                <param name="input" type="data" format="fasta" label="FASTA sequences" />
            </when>
        </conditional>
        <param name="method01" type="select" display="checkboxes" multiple="true" label="Pairwise Structual Method">
            <option value="sap_pair">sap_pair</option>
            <option value="TMalign_pair">TMalign_pair</option>
            <option value="mustang_pair">mustang_pair</option>
        </param>
        <param name="method02" type="select" display="checkboxes" multiple="true" label="Multiple Sequence Alignment Methods">
            <option value="pcma_msa">pcma_msa</option>
            <option value="clustalw_msa">clustalw_msa</option>
            <option value="dialigntx_msa">dialigntx_msa</option>
            <option value="poa_msa">poa_msa</option>
            <option value="muscle_msa">muscle_msa</option>
            <option value="probcons_msa">probcons_msa</option>
            <option value="t_coffee_msa">t_coffee_msa</option>
            <option value="amap_msa">amap_msa</option>
            <option value="kalign_msa">kalign_msa</option>
        </param>
        <param name="method03" type="select" display="checkboxes" multiple="true" label="Pairwise Sequence Alignment Methods">
            <option value="fast_pair">fast_pair</option>
            <option value="clustalw_pair">clustalw_pair</option>
            <option value="lalign_id_pair">lalign_id_pair</option>
            <option value="slow_pair">slow_pair</option>
            <option value="proba_pair">proba_pair</option>
        </param>
        <param name="outputs" type="select" multiple="true" optional="false" display="checkboxes" label="Additional outputs">
            <option value="cigar">CIGAR</option>
            <option value="clustalw_aln">clustalw_aln</option>
            <option value="dnd" selected="true">dnd</option>
            <option value="fasta_aln">fasta_aln</option>
            <option value="fasta_seq">fasta_seq</option>
            <option value="msf_aln">msf_aln</option>
            <option value="phylip">phylip</option>
            <option value="pir_aln">pir_aln</option>
            <option value="pir_seq">pir_seq</option>
            <option value="score_ascii">score_ascii</option>
            <option value="score_html">score_html</option>
        </param>
    </inputs>
    <outputs>
        <data name="cigar" format="tabular" label="${tool.name} on ${on_string}: cigar" >
            <filter>'cigar' in outputs</filter>
        </data>
        <data name="clustalw_aln" format="clustalw" label="${tool.name} on ${on_string}: clustalw_aln" from_work_dir="t_coffee_out.clustalw_aln">
            <filter>'clustalw_aln' in outputs</filter>
        </data>
        <data name="dnd" format="nhx" label="${tool.name} on ${on_string}: newick.dnd" from_work_dir="t_coffee_out.dnd">
            <filter>'dnd' in outputs</filter>
        </data>
        <data name="fasta_aln" format="fasta" label="${tool.name} on ${on_string}: fasta_aln" from_work_dir="t_coffee_out.fasta_aln">
            <filter>'fasta_aln' in outputs</filter>
        </data>
        <data name="fasta_seq" format="fasta" label="${tool.name} on ${on_string}: fasta_seq" from_work_dir="t_coffee_out.fasta_seq">
            <filter>'fasta_seq' in outputs</filter>
        </data>
        <data name="msf_aln" format="msf" label="${tool.name} on ${on_string}: msf_aln" from_work_dir="t_coffee_out.msf_aln">
            <filter>'msf_aln' in outputs</filter>
        </data>
        <data name="phylip" format="phyloxml" label="${tool.name} on ${on_string}: phylip" from_work_dir="t_coffee_out.phylip">
            <filter>'phylip' in outputs</filter>
        </data>
        <data name="pir_aln" format="pir" label="${tool.name} on ${on_string}: pir_aln" from_work_dir="t_coffee_out.pir_aln">
            <filter>'pir_aln' in outputs</filter>
        </data>
        <data name="pir_seq" format="pir" label="${tool.name} on ${on_string}: pir_seq" from_work_dir="t_coffee_out.pir_seq">
            <filter>'pir_seq' in outputs</filter>
        </data>
        <data name="score_ascii" format="ascii" label="${tool.name} on ${on_string}: score_ascii" from_work_dir="t_coffee_out.score_ascii">
            <filter>'score_ascii' in outputs</filter>
        </data>
        <data name="score_html" format="html" label="${tool.name} on ${on_string}: score_html" from_work_dir="t_coffee_out.score_html">
            <filter>'score_html' in outputs</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="filter_fasta" value="no" />
            <param name="input" value="input.fasta" ftype="fasta" />
            <param name="method02" value="clustalw_msa" />
            <param name="outputs" value="fasta_aln" />
            <output name="fasta_aln" file="output1.fasta" />
        </test>
        <test>
            <param name="filter_fasta" value="yes" />
            <param name="fasta_input" value="input.fasta" ftype="fasta" />
            <param name="identifiers" value="ids.txt" ftype="txt" />
            <param name="method02" value="clustalw_msa" />
            <param name="outputs" value="cigar" />
            <output name="cigar" file="cigar.tabular" />
        </test>
    </tests>
    <help>
**What it does**

This tool is a wrapper for the T-Coffee multiple sequence alignment suite. The input is a set of sequences in FASTA format. Apart from running on the complete FASTA input, it can also run on a subset of sequences by providing a list of the FASTA IDs.

This wrapper offers selected advanced T-Coffee options like the selection of the alignment methods to use: ''Pairwise Structual Method'', ''Multiple Sequence Alignment Methods'' or ''Pairwise Sequence Alignment Methods''.

The T-Coffee documentation can be found at http://www.tcoffee.org/Projects/tcoffee/ .

**Example**

Suppose you have 5 sequences in FASTA format::

    >1aboA
    NLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPS
    NYITPVN
    >1ycsB
    KGVIYALWDYEPQNDDELPMKEGDCMTIIHREDEDEIEWWWARLNDKEGY
    VPRNLLGLYP
    >1pht
    GYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPEEIG
    WLNGYNETTGERGDFPGTYVEYIGRKKISP
    >1vie
    DRVRKKSGAAWQGQIVGWYCTNLTPEGYAVESEAHPGSVQIYPVAALERI
    N
    >1ihvA
    NFRVYYRDSRDPVWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRD

By selecting "Yes" in output fasta_aln in the wrapper, the user will obtain the multiple alignment in FASTA format::

    >1aboA
    NL-FVA---LYDFVASGDNTLSITKGEKLR-------VLGYN-------H
    NGEWCEA--QTKN-GQGWVPSNYIT------PVN
    >1ycsB
    KGVIYA---LWDYEPQNDDELPMKEGDCMT-------IIHREDE-----D
    EIEWWWA--RLND-KEGYVPRNLLG------LYP
    >1pht
    GYQYRA---LYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPE
    EIGWLNGYNETTG-ERGDFPGTYVEYIGRKKISP
    >1vie
    DR-----------VRK--KSGAAWQGQIVGWYCTNLTPEGYAVE------
    ------S--EAHPGSVQIYPVAALE------RIN
    >1ihvA
    NF-RVYYRDSRDPVWKGPA-KLLWKGEGAV-------VIQDN-------S
    DI--------------KVVPRRKAK-----IIRD
    </help>
    <citations>
        <citation type="doi">10.1006/jmbi.2000.4042</citation>
    </citations>
</tool>