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1 <tool id="rbc_mafft" name="MAFFT" version="7.221.3">
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2
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2 <description>Add sequence to a alignment already done.</description>
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3 <requirements>
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4 <requirement type="package" version="7.221">mafft</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
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8 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
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9 </stdio>
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10 <version_command>
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11 <![CDATA[
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12 mafft --version
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13 ]]>
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14 </version_command>
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15 <command>
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16 <![CDATA[
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17 mafft --thread \${GALAXY_SLOTS:-1} --add $seqtoadd --reorder $existingalignment > $outputAlignment
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param name="seqtoadd" type="data" format="fasta" label="Sequences to add" help="Sequences to add in FASTA format."/>
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22 <param name="existingalignment" type="data" format="fasta" label="Alignment already done" help="Multi-alignment in FASTA format."/>
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23 </inputs>
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24 <outputs>
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3
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25 <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string}">
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26 <change_format>
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27 <when input="outputFormat" value="--clustalout" format="clustal"/>
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28 <when input="outputFormat" value="--phylipout" format="phylip"/>
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29 </change_format>
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30 </data>
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0
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31 </outputs>
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32 <help>
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33 <![CDATA[
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34 **What it does**
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35
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36 MAFFT is a multiple sequence alignment program for unix-like operating systems.
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37 It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences),
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38 FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
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39
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40 Using only to add new sequence in alignment already done.
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41
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42 ]]>
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43 </help>
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44 <citations>
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45 <citation type="doi">10.1093/molbev/mst010</citation>
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46 </citations>
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47 </tool>
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