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comparison mafft.xml @ 0:a4e086689fae draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 1fc2105007248c6b9460c0f3a98e6589477d0b13
author rnateam
date Thu, 18 Jun 2015 08:59:56 -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 #elif $cond_flavour.flavourType == 'custom'
20 ### full parameter options
21 mafft
22 #end if
23
24 ## specify threads to use
25 --thread \${GALAXY_SLOTS:-1}
26
27 #if $outputFormat.value == 'clustalw'
28 --clustalout
29 #end if
30
31 $inputSequences >
32
33 #if $outputFormat.value == 'fasta'
34 $outputFasta
35 #elif $outputFormat.value == 'clustalw'
36 $outputClustalW
37 #end if
38 ]]>
39 </command>
40 <inputs>
41 <param name="inputSequences" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/>
42 <conditional name="cond_flavour">
43 <param name="flavourType" type="select" label="MAFFT flavour" help="Run mafft with pre-defined input parameters. Specification of these parameters can be found in the help section.">
44 <option value="mafft-fftns" selected="true">fftns</option>
45 <option value="mafft-fftnsi">fftnsi</option>
46 <option value="mafft-nwns">nwns</option>
47 <option value="mafft-nwnsi">nwnsi</option>
48 <option value="mafft-einsi">einsi</option>
49 <option value="mafft-ginsi">ginsi</option>
50 <option value="mafft-linsi">linsi</option>
51 <option value="mafft-qinsi">qinsi</option>
52 <option value="mafft-xinsi">xinsi</option>
53 <!-- <option value="custom">Custom Parameters</option> this should trigger tweaking of all parameters -->
54 </param>
55 <when value="mafft-fftns"/>
56 <when value="mafft-fftnsi"/>
57 <when value="mafft-nwns"/>
58 <when value="mafft-nwnsi"/>
59 <when value="mafft-einsi"/>
60 <when value="mafft-ginsi"/>
61 <when value="mafft-linsi"/>
62 <when value="mafft-qinsi"/>
63 <when value="mafft-xinsi"/>
64 </conditional>
65 <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW">
66 <option value="fasta" selected="true">FASTA</option>
67 <option value="clustalw">ClustalW</option>
68 </param>
69 </inputs>
70 <outputs>
71 <data format="fasta" name="outputFasta" label="${tool.name} on ${on_string}">
72 <filter>outputFormat == 'fasta'</filter>
73 </data>
74 <data format="clustal" name="outputClustalW" label="${tool.name} on ${on_string}">
75 <filter>outputFormat == 'clustalw'</filter>
76 </data>
77 </outputs>
78 <tests>
79 <test>
80 <param name="inputSequences" value="sample.fa"/>
81 <param name="flavourType" value="mafft-fftns"/>
82 <param name="outputFormat" value="fasta"/>
83 <output name="outputFasta" ftype="fasta" file="mafft_fftns_result.aln"/>
84 </test>
85 <test>
86 <param name="inputSequences" value="sample.fa"/>
87 <param name="flavourType" value="mafft-nwns"/>
88 <param name="outputFormat" value="clustalw"/>
89 <output name="outputClustalW" ftype="clustal" file="mafft_nwns_result.aln"/>
90 </test>
91 </tests>
92 <help>
93 <![CDATA[
94 **What it does**
95
96 MAFFT is a multiple sequence alignment program for unix-like operating systems.
97 It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences),
98 FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
99
100 From the MAFFT man page, an overview of the different predefined flavours of the tool.
101
102 **Accuracy-oriented methods:**
103
104 - L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information):
105
106 - mafft --localpair --maxiterate 1000 input [> output]
107
108 - G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information):
109
110 - mafft --globalpair --maxiterate 1000 input [> output]
111
112 - E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences):
113
114 - mafft --ep 0 --genafpair --maxiterate 1000 input [> output]. For E-INS-i, the --ep 0 option is recommended to allow large gaps.
115
116
117 **Speed-oriented methods:**
118
119 - FFT-NS-i (iterative refinement method; two cycles only):
120
121 - mafft --retree 2 --maxiterate 2 input [> output]
122
123 - FFT-NS-i (iterative refinement method; max. 1000 iterations):
124
125 - mafft --retree 2 --maxiterate 1000 input [> output]
126
127 - FFT-NS-2 (fast; progressive method):
128
129 - mafft --retree 2 --maxiterate 0 input [> output]
130
131 - FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree):
132
133 - mafft --retree 1 --maxiterate 0 input [> output]
134
135 - NW-NS-i (iterative refinement method without FFT approximation; two cycles only):
136
137 - mafft --retree 2 --maxiterate 2 --nofft input [> output]
138
139 - NW-NS-2 (fast; progressive method without the FFT approximation):
140
141 - mafft --retree 2 --maxiterate 0 --nofft input [> output]
142
143 - NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm):
144
145 - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output]
146
147 ]]>
148 </help>
149 <citations>
150 <citation type="doi">10.1093/molbev/mst010</citation>
151 </citations>
152 </tool>