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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 $outputFormat > $outputAlignment;
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param name="seqtoadd" type="data" format="fasta" label="Sequences to add" help="Sequences to add in FASTA format."/>
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22 <param name="existingalignment" type="data" format="fasta" label="Alignment already done" help="Multi-alignment in FASTA format."/>
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23 <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW or Phylip">
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24 <option value="" selected="true">FASTA</option>
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25 <option value="--clustalout">ClustalW</option>
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26 <option value="--phylipout">Phylip</option>
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27 </param>
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28 </inputs>
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29 <outputs>
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3
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30 <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string}">
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31 <change_format>
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32 <when input="outputFormat" value="--clustalout" format="clustal"/>
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33 <when input="outputFormat" value="--phylipout" format="phylip"/>
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34 </change_format>
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35 </data>
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36 </outputs>
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37 <help>
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38 <![CDATA[
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39 **What it does**
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40
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41 MAFFT is a multiple sequence alignment program for unix-like operating systems.
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42 It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences),
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43 FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
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44
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45 Using only to add new sequence in alignment already done.
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46
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47 ]]>
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48 </help>
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49 <citations>
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50 <citation type="doi">10.1093/molbev/mst010</citation>
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51 </citations>
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52 </tool>
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