annotate tcoffee.xml @ 16:e65eb41717b4 draft default tip

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<tool id="T_coffee" name="T-COFFEE" version="10.00.r1613">
  <description>multiple aligment</description>
  <command interpreter="perl">
    tcoffee.pl $input $method01 $method02 $method03 $dnd $msf_aln $clustalw_aln $pir_aln $fasta_aln $phylip $pir_seq $fasta_seq $score_ascii $score_html
  </command>

  <inputs>
    <param format="fasta" name="input" type="data" label="Source file"/>
    <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="format_output_dnd" type="select" display="radio" label="Output newick">
        <option value="no">No</option>
        <option value="yes">Yes</option>
    </param>
    <param name="format_output_msf_aln" type="select" display="radio" label="Output msf_aln">
        <option value="no">No</option>
        <option value="yes">Yes</option>
    </param>
    <param name="format_output_clustalw_aln" type="select" display="radio" label="Output clustalw_aln">
        <option value="no">No</option>
        <option value="yes">Yes</option>
    </param>
    <param name="format_output_pir_aln" type="select" display="radio" label="Output pir_aln">
        <option value="no">No</option>
        <option value="yes">Yes</option>
    </param>
    <param name="format_output_fasta_aln" type="select" display="radio" label="Output fasta_aln">
        <option value="no">No</option>
        <option value="yes">Yes</option>
    </param>
    <param name="format_output_phylip" type="select" display="radio" label="Output phylip">
        <option value="no">No</option>
        <option value="yes">Yes</option>
    </param>
    <param name="format_output_pir_seq" type="select" display="radio" label="Output pir_seq">
        <option value="no">No</option>
        <option value="yes">Yes</option>
    </param>
    <param name="format_output_fasta_seq" type="select" display="radio" label="Output fasta_seq">
        <option value="no">No</option>
        <option value="yes">Yes</option>
    </param>
    <param name="format_output_score_ascii" type="select" display="radio" label="Output score_ascii">
        <option value="no">No</option>
        <option value="yes">Yes</option>
    </param>
    <param name="format_output_score_html" type="select" display="radio" label="Output score_html">
        <option value="no">No</option>
        <option value="yes">Yes</option>
    </param>
  </inputs>

  <outputs>
    <data format="nhx" name="dnd" label="${tool.name} on ${on_string}: newick.dnd" >
      <filter>format_output_dnd == "yes"</filter>
    </data>
    <data format="msf" name="msf_aln" label="${tool.name} on ${on_string}: msf_aln" >
      <filter>format_output_msf_aln == "yes"</filter>
    </data>
    <data format="clustalw" name="clustalw_aln" label="${tool.name} on ${on_string}: clustalw_aln" >
      <filter>format_output_clustalw_aln == "yes"</filter>
    </data>
    <data format="pir" name="pir_aln" label="${tool.name} on ${on_string}: pir_aln" >
      <filter>format_output_pir_aln == "yes"</filter>
    </data>
    <data format="fasta" name="fasta_aln" label="${tool.name} on ${on_string}: fasta_aln" >
      <filter>format_output_fasta_aln == "yes"</filter>
    </data>
    <data format="phyloxml" name="phylip" label="${tool.name} on ${on_string}: phylip" >
      <filter>format_output_phylip == "yes"</filter>
    </data>
    <data format="pir" name="pir_seq" label="${tool.name} on ${on_string}: pir_seq" >
      <filter>format_output_pir_seq == "yes"</filter>
    </data>
    <data format="fasta" name="fasta_seq" label="${tool.name} on ${on_string}: fasta_seq" >
      <filter>format_output_fasta_seq == "yes"</filter>
    </data>
    <data format="ascii" name="score_ascii" label="${tool.name} on ${on_string}: score_ascii" >
      <filter>format_output_score_ascii == "yes"</filter>
    </data>
    <data format="html" name="score_html" label="${tool.name} on ${on_string}: score_html" >
      <filter>format_output_score_html == "yes"</filter>
    </data>
  </outputs>
  <help>
    
    **Requeriments**
   
    You must install T_coffee version "10.00.r1613" in your computer.
   
-----
   
    **What it does**

    This tool is a wrapper for the T-Coffee multiple alignment suite. The input is a set of sequences in FASTA format that must be uploaded to Galaxy if not obtained using Galaxy tools.
   
    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/documentation
   
-----

    **Example**

    Suppose you have five 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>
  <tests>
    <test>
      <param name="input" value="3.fasta" ftype= "fasta"/>
      <param name="format_output_fasta_aln" value="yes"/>
      <output name="fasta_aln" file="out3.fasta" ftype= "fasta"/>
    </test>
  </tests>
  <requirements>
    <requirement type="package" version="10.00.r1613">T-COFFEE</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" level="fatal" description="Error" />
  </stdio>
  

</tool>