# HG changeset patch
# User ayllon
# Date 1412869368 14400
# Node ID e65eb41717b455880ff046930c415e431be4d344
# Parent  b448d75d58eb5952d1d0379728d9eb0d75560dfd
Uploaded

diff -r b448d75d58eb -r e65eb41717b4 tcoffee.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tcoffee.xml	Thu Oct 09 11:42:48 2014 -0400
@@ -0,0 +1,182 @@
+<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>