Mercurial > repos > ayllon > tcoffee
changeset 9:c9fc8574e6f1 draft
Uploaded
author | ayllon |
---|---|
date | Sun, 07 Sep 2014 04:42:36 -0400 (2014-09-07) |
parents | 620741ec77ed |
children | 6641a449026d |
files | tcoffee.xml |
diffstat | 1 files changed, 171 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tcoffee.xml Sun Sep 07 04:42:36 2014 -0400 @@ -0,0 +1,171 @@ +<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> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + +</tool>