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comparison mafft.xml @ 0:a56bda3448b1 draft

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author p.lucas
date Thu, 02 May 2019 05:40:01 -0400
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1 <tool id="rbc_mafft" name="MAFFT" version="7.221.3">
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 mafft --thread \${GALAXY_SLOTS:-1} --add $seqtoadd --reorder $existingalignment > $outputAlignment
18 ]]>
19 </command>
20 <inputs>
21 <param name="seqtoadd" type="data" format="fasta" label="Sequences to add" help="Sequences to add in FASTA format."/>
22 <param name="existingalignment" type="data" format="fasta" label="Alignment already done" help="Multi-alignment in FASTA format."/>
23 </inputs>
24 <outputs>
25 <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string}"/>
26 </outputs>
27 <help>
28 <![CDATA[
29 **What it does**
30
31 MAFFT is a multiple sequence alignment program for unix-like operating systems.
32 It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences),
33 FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
34
35 Using only to add new sequence in alignment already done.
36
37 ]]>
38 </help>
39 <citations>
40 <citation type="doi">10.1093/molbev/mst010</citation>
41 </citations>
42 </tool>