Mercurial > repos > rnateam > mafft
comparison mafft.xml @ 0:8817d3a35fac draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 4e6896fc58abc9a6f90d97aaf80fde006a071a7d-dirty
author | rnateam |
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date | Tue, 16 Jun 2015 10:54:16 -0400 |
parents | |
children | 95526e9e3808 |
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1 <tool id="rbc_mafft" name="MAFFT" version="7.221.0"> | |
2 <description>Multiple alignment program for amino acid or nucleotide sequences</description> | |
3 <requirements> | |
4 <requirement type="package" version="7.221">mafft</requirement> | |
5 </requirements> | |
6 <stdio> | |
7 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> | |
8 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" /> | |
9 </stdio> | |
10 <version_command> | |
11 <![CDATA[ | |
12 mafft --version | |
13 ]]> | |
14 </version_command> | |
15 <command> | |
16 <![CDATA[ | |
17 #if $cond_flavour.flavourType != 'custom' | |
18 $cond_flavour.flavourType | |
19 #else | |
20 ### full parameter options | |
21 mafft | |
22 #end if | |
23 | |
24 #if $cond_outformat.outputFormat == 'clustalw' | |
25 --clustalout | |
26 #end if | |
27 | |
28 $inputSequences > | |
29 | |
30 #if $cond_outformat.outputFormat == 'fasta' | |
31 $outputFasta | |
32 #else ## $cond_outformat.outputFormat == 'clustalw' | |
33 $outputClustalW | |
34 #end if | |
35 ]]> | |
36 </command> | |
37 <inputs> | |
38 <param name="inputSequences" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/> | |
39 <conditional name="cond_flavour"> | |
40 <param name="flavourType" type="select" label="MAFFT flavour" help="Run mafft with pre-defined input parameters. Specification of these parameters can be found in the help section."> | |
41 <option value="mafft-fftns" selected="true">fftns</option> | |
42 <option value="mafft-fftnsi">fftnsi</option> | |
43 <option value="mafft-nwns">nwns</option> | |
44 <option value="mafft-nwnsi">nwnsi</option> | |
45 <option value="mafft-einsi">einsi</option> | |
46 <option value="mafft-ginsi">ginsi</option> | |
47 <option value="mafft-linsi">linsi</option> | |
48 <option value="mafft-qinsi">qinsi</option> | |
49 <option value="mafft-xinsi">xinsi</option> | |
50 <option value="custom">Custom Parameters</option> | |
51 </param> | |
52 <when value="mafft-fftns"/> | |
53 <when value="mafft-fftnsi"/> | |
54 <when value="mafft-nwns"/> | |
55 <when value="mafft-nwnsi"/> | |
56 <when value="mafft-einsi"/> | |
57 <when value="mafft-ginsi"/> | |
58 <when value="mafft-linsi"/> | |
59 <when value="mafft-qinsi"/> | |
60 <when value="mafft-xinsi"/> | |
61 <when value="custom"/> | |
62 </conditional> | |
63 <conditional name="cond_outformat"> | |
64 <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW"> | |
65 <option value="fasta" selected="true">FASTA</option> | |
66 <option value="clustalw">ClustalW</option> | |
67 </param> | |
68 <when value="fasta"/> | |
69 <when value="clustalw"/> | |
70 </conditional> | |
71 </inputs> | |
72 <outputs> | |
73 <data format="fasta" name="outputFasta" label="${tool.name} on ${on_string}"> | |
74 <filter>(cond_outformat['outputFormat'] == 'fasta')</filter> | |
75 </data> | |
76 <data format="clustal" name="outputClustalW" label="${tool.name} on ${on_string}"> | |
77 <filter>(cond_outformat['outputFormat'] == 'clustalw')</filter> | |
78 </data> | |
79 </outputs> | |
80 <tests> | |
81 <test> | |
82 <param name="inputSequences" value="sample"/> | |
83 <param name="flavourType" value="fftns"/> | |
84 <param name="outputFormat" value="fasta"/> | |
85 <output name="outputFasta" file="sample.fftns2"/> | |
86 </test> | |
87 </tests> | |
88 <help> | |
89 <![CDATA[ | |
90 **What it does** | |
91 | |
92 MAFFT is a multiple sequence alignment program for unix-like operating systems. | |
93 It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), | |
94 FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc. | |
95 | |
96 From the MAFFT man page, an overview of the different predefined flavours of the tool. | |
97 | |
98 **Accuracy-oriented methods:** | |
99 | |
100 - L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information): | |
101 | |
102 - mafft --localpair --maxiterate 1000 input [> output] | |
103 | |
104 - G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information): | |
105 | |
106 - mafft --globalpair --maxiterate 1000 input [> output] | |
107 | |
108 - E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences): | |
109 | |
110 - mafft --ep 0 --genafpair --maxiterate 1000 input [> output]. For E-INS-i, the --ep 0 option is recommended to allow large gaps. | |
111 | |
112 | |
113 **Speed-oriented methods:** | |
114 | |
115 - FFT-NS-i (iterative refinement method; two cycles only): | |
116 | |
117 - mafft --retree 2 --maxiterate 2 input [> output] | |
118 | |
119 - FFT-NS-i (iterative refinement method; max. 1000 iterations): | |
120 | |
121 - mafft --retree 2 --maxiterate 1000 input [> output] | |
122 | |
123 - FFT-NS-2 (fast; progressive method): | |
124 | |
125 - mafft --retree 2 --maxiterate 0 input [> output] | |
126 | |
127 - FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree): | |
128 | |
129 - mafft --retree 1 --maxiterate 0 input [> output] | |
130 | |
131 - NW-NS-i (iterative refinement method without FFT approximation; two cycles only): | |
132 | |
133 - mafft --retree 2 --maxiterate 2 --nofft input [> output] | |
134 | |
135 - NW-NS-2 (fast; progressive method without the FFT approximation): | |
136 | |
137 - mafft --retree 2 --maxiterate 0 --nofft input [> output] | |
138 | |
139 - NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm): | |
140 | |
141 - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output] | |
142 | |
143 ]]> | |
144 </help> | |
145 <citations> | |
146 <citation type="doi">10.1093/molbev/mst010</citation> | |
147 <citation type="doi">10.1093/nar/gkt389</citation> | |
148 <citation type="doi">10.1093/bioinformatics/bts578</citation> | |
149 <citation type="doi">10.1093/bioinformatics/btq224</citation> | |
150 <citation type="doi">10.1007/978-1-59745-251-9_3</citation> | |
151 <citation type="doi">10.1186/1471-2105-9-212</citation> | |
152 <citation type="doi">10.1093/bib/bbn013</citation> | |
153 <citation type="doi">10.1093/bioinformatics/btl592</citation> | |
154 <citation type="doi">10.1093/nar/gki198</citation> | |
155 <citation type="doi">10.1093/nar/gkf436</citation> | |
156 </citations> | |
157 </tool> |