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comparison mafft.xml @ 0:8817d3a35fac draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 4e6896fc58abc9a6f90d97aaf80fde006a071a7d-dirty
author rnateam
date Tue, 16 Jun 2015 10:54:16 -0400
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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>