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comparison t_coffee.xml @ 0:794a6e864a96 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 230ae552ddeb1bfdef3a09becaa5c6d373529a05-dirty
author earlhaminst
date Thu, 15 Dec 2016 11:04:25 -0500
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-1:000000000000 0:794a6e864a96
1 <tool id="t_coffee" name="T-Coffee" version="11.0.8">
2 <description>multiple sequence alignment</description>
3 <requirements>
4 <requirement type="package" version="11.0.8">t_coffee</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" level="fatal" />
8 </stdio>
9 <version_command>
10 t_coffee -version | grep Version
11 </version_command>
12 <command>
13 <![CDATA[
14 #if str($input_type.filter_fasta) == 'yes'
15 #set $input = '-infile=stdin'
16 python '$__tool_directory__/filter_by_fasta_ids.py' '$input_type.identifiers' '$input_type.fasta_input' |
17 #end if
18
19 #set $method_opt = ''
20 #if $method01
21 #set $method_opt += str($method01) + ','
22 #end if
23 #if $method02
24 #set $method_opt += str($method02) + ','
25 #end if
26 #if $method03
27 #set $method_opt += str($method03) + ','
28 #end if
29 #if $method_opt
30 #set $method_opt = '-method ' + $method_opt[:-1]
31 #end if
32
33 #set $output_opt = ''
34 #if $outputs
35 #set $outputs_arr = str($outputs).split(',')
36 #for $o in $outputs_arr
37 #if $o not in ['cigar', 'dnd']
38 #set $output_opt += $o + ','
39 #end if
40 #end for
41 #if 'cigar' in $outputs_arr and 'fasta_aln' not in $outputs_arr
42 #set $output_opt += 'fasta_aln,'
43 #end if
44 #else
45 #set $outputs_arr = []
46 #end if
47 #if $output_opt
48 #set $output_opt = '-output ' + $output_opt[:-1]
49 #end if
50
51 t_coffee '$input' $method_opt $output_opt -n_core \${GALAXY_SLOTS:-1} -run_name t_coffee_out -quiet
52
53 #if 'cigar' in $outputs_arr
54 && perl '$__tool_directory__/t_coffee_to_cigar.pl' t_coffee_out.fasta_aln > '$cigar'
55 #end if
56 ]]>
57 </command>
58 <inputs>
59 <conditional name="input_type">
60 <param name="filter_fasta" type="select" label="Filter FASTA input?">
61 <option value="no">No</option>
62 <option value="yes">Yes</option>
63 </param>
64 <when value="yes">
65 <param name="fasta_input" type="data" format="fasta" label="FASTA sequences" />
66 <param name="identifiers" type="data" format="txt" label="List of FASTA sequence IDs" />
67 </when>
68 <when value="no">
69 <param name="input" type="data" format="fasta" label="FASTA sequences" />
70 </when>
71 </conditional>
72 <param name="method01" type="select" display="checkboxes" multiple="true" label="Pairwise Structual Method">
73 <option value="sap_pair">sap_pair</option>
74 <option value="TMalign_pair">TMalign_pair</option>
75 <option value="mustang_pair">mustang_pair</option>
76 </param>
77 <param name="method02" type="select" display="checkboxes" multiple="true" label="Multiple Sequence Alignment Methods">
78 <option value="pcma_msa">pcma_msa</option>
79 <option value="clustalw_msa">clustalw_msa</option>
80 <option value="dialigntx_msa">dialigntx_msa</option>
81 <option value="poa_msa">poa_msa</option>
82 <option value="muscle_msa">muscle_msa</option>
83 <option value="probcons_msa">probcons_msa</option>
84 <option value="t_coffee_msa">t_coffee_msa</option>
85 <option value="amap_msa">amap_msa</option>
86 <option value="kalign_msa">kalign_msa</option>
87 </param>
88 <param name="method03" type="select" display="checkboxes" multiple="true" label="Pairwise Sequence Alignment Methods">
89 <option value="fast_pair">fast_pair</option>
90 <option value="clustalw_pair">clustalw_pair</option>
91 <option value="lalign_id_pair">lalign_id_pair</option>
92 <option value="slow_pair">slow_pair</option>
93 <option value="proba_pair">proba_pair</option>
94 </param>
95 <param name="outputs" type="select" multiple="true" optional="false" display="checkboxes" label="Additional outputs">
96 <option value="cigar">CIGAR</option>
97 <option value="clustalw_aln">clustalw_aln</option>
98 <option value="dnd" selected="true">dnd</option>
99 <option value="fasta_aln">fasta_aln</option>
100 <option value="fasta_seq">fasta_seq</option>
101 <option value="msf_aln">msf_aln</option>
102 <option value="phylip">phylip</option>
103 <option value="pir_aln">pir_aln</option>
104 <option value="pir_seq">pir_seq</option>
105 <option value="score_ascii">score_ascii</option>
106 <option value="score_html">score_html</option>
107 </param>
108 </inputs>
109 <outputs>
110 <data name="cigar" format="tabular" label="${tool.name} on ${on_string}: cigar" >
111 <filter>'cigar' in outputs</filter>
112 </data>
113 <data name="clustalw_aln" format="clustalw" label="${tool.name} on ${on_string}: clustalw_aln" from_work_dir="t_coffee_out.clustalw_aln">
114 <filter>'clustalw_aln' in outputs</filter>
115 </data>
116 <data name="dnd" format="nhx" label="${tool.name} on ${on_string}: newick.dnd" from_work_dir="t_coffee_out.dnd">
117 <filter>'dnd' in outputs</filter>
118 </data>
119 <data name="fasta_aln" format="fasta" label="${tool.name} on ${on_string}: fasta_aln" from_work_dir="t_coffee_out.fasta_aln">
120 <filter>'fasta_aln' in outputs</filter>
121 </data>
122 <data name="fasta_seq" format="fasta" label="${tool.name} on ${on_string}: fasta_seq" from_work_dir="t_coffee_out.fasta_seq">
123 <filter>'fasta_seq' in outputs</filter>
124 </data>
125 <data name="msf_aln" format="msf" label="${tool.name} on ${on_string}: msf_aln" from_work_dir="t_coffee_out.msf_aln">
126 <filter>'msf_aln' in outputs</filter>
127 </data>
128 <data name="phylip" format="phyloxml" label="${tool.name} on ${on_string}: phylip" from_work_dir="t_coffee_out.phylip">
129 <filter>'phylip' in outputs</filter>
130 </data>
131 <data name="pir_aln" format="pir" label="${tool.name} on ${on_string}: pir_aln" from_work_dir="t_coffee_out.pir_aln">
132 <filter>'pir_aln' in outputs</filter>
133 </data>
134 <data name="pir_seq" format="pir" label="${tool.name} on ${on_string}: pir_seq" from_work_dir="t_coffee_out.pir_seq">
135 <filter>'pir_seq' in outputs</filter>
136 </data>
137 <data name="score_ascii" format="ascii" label="${tool.name} on ${on_string}: score_ascii" from_work_dir="t_coffee_out.score_ascii">
138 <filter>'score_ascii' in outputs</filter>
139 </data>
140 <data name="score_html" format="html" label="${tool.name} on ${on_string}: score_html" from_work_dir="t_coffee_out.score_html">
141 <filter>'score_html' in outputs</filter>
142 </data>
143 </outputs>
144 <tests>
145 <test>
146 <param name="filter_fasta" value="no" />
147 <param name="input" value="input.fasta" ftype="fasta" />
148 <param name="method02" value="clustalw_msa" />
149 <param name="outputs" value="fasta_aln" />
150 <output name="fasta_aln" file="output1.fasta" />
151 </test>
152 <test>
153 <param name="filter_fasta" value="yes" />
154 <param name="fasta_input" value="input.fasta" ftype="fasta" />
155 <param name="identifiers" value="ids.txt" ftype="txt" />
156 <param name="method02" value="clustalw_msa" />
157 <param name="outputs" value="cigar" />
158 <output name="cigar" file="cigar.tabular" />
159 </test>
160 </tests>
161 <help>
162 **What it does**
163
164 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.
165
166 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''.
167
168 The T-Coffee documentation can be found at http://www.tcoffee.org/Projects/tcoffee/ .
169
170 **Example**
171
172 Suppose you have 5 sequences in FASTA format::
173
174 >1aboA
175 NLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPS
176 NYITPVN
177 >1ycsB
178 KGVIYALWDYEPQNDDELPMKEGDCMTIIHREDEDEIEWWWARLNDKEGY
179 VPRNLLGLYP
180 >1pht
181 GYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPEEIG
182 WLNGYNETTGERGDFPGTYVEYIGRKKISP
183 >1vie
184 DRVRKKSGAAWQGQIVGWYCTNLTPEGYAVESEAHPGSVQIYPVAALERI
185 N
186 >1ihvA
187 NFRVYYRDSRDPVWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRD
188
189 By selecting "Yes" in output fasta_aln in the wrapper, the user will obtain the multiple alignment in FASTA format::
190
191 >1aboA
192 NL-FVA---LYDFVASGDNTLSITKGEKLR-------VLGYN-------H
193 NGEWCEA--QTKN-GQGWVPSNYIT------PVN
194 >1ycsB
195 KGVIYA---LWDYEPQNDDELPMKEGDCMT-------IIHREDE-----D
196 EIEWWWA--RLND-KEGYVPRNLLG------LYP
197 >1pht
198 GYQYRA---LYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPE
199 EIGWLNGYNETTG-ERGDFPGTYVEYIGRKKISP
200 >1vie
201 DR-----------VRK--KSGAAWQGQIVGWYCTNLTPEGYAVE------
202 ------S--EAHPGSVQIYPVAALE------RIN
203 >1ihvA
204 NF-RVYYRDSRDPVWKGPA-KLLWKGEGAV-------VIQDN-------S
205 DI--------------KVVPRRKAK-----IIRD
206 </help>
207 <citations>
208 <citation type="doi">10.1006/jmbi.2000.4042</citation>
209 </citations>
210 </tool>